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3 <title>MayaChemTools:Code:Atom.pm</title>
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13 <pre>
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14 <a name="package-Atom-"></a> 1 <span class="k">package </span><span class="i">Atom</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: Atom.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: 1.62 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">Storable</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">PeriodicTable</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">Vector</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">MathUtil</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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53 40 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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54 41
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55 42 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span>
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56 43
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57 44 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span>
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58 45 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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59 46 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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60 47
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61 48 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
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62 49
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63 50 <span class="c"># Setup class variables...</span>
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64 51 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="cm">,</span> <span class="i">%MDLValenceModelDataMap</span><span class="cm">,</span> <span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span>
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65 52 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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66 53
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67 54 <span class="c"># Overload Perl functions...</span>
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68 55 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyAtom'</span><span class="sc">;</span>
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69 56
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70 57 <span class="c"># Class constructor...</span>
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71 <a name="new-"></a> 58 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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72 59 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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73 60
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74 61 <span class="c"># Initialize object...</span>
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75 62 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span>
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76 63 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span>
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77 64 <span class="i">$This</span><span class="i">->_InitializeAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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78 65
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79 66 <span class="i">$This</span><span class="i">->_InitializeAtomProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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80 67
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81 68 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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82 69 <span class="s">}</span>
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83 70
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84 71 <span class="c"># Initialize object data...</span>
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85 <a name="_InitializeAtom-"></a> 72 <span class="k">sub </span><span class="m">_InitializeAtom</span> <span class="s">{</span>
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86 73 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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87 74 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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88 75
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89 76 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span>
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90 77 <span class="c"># are implemented on-demand using ObjectProperty class.</span>
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91 78 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span>
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92 79 <span class="i">$This</span>->{<span class="w">Name</span>} = <span class="q">"Atom ${ObjectID}"</span><span class="sc">;</span>
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93 80 <span class="i">$This</span>->{<span class="w">AtomSymbol</span>} = <span class="q">''</span><span class="sc">;</span>
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94 81 <span class="i">$This</span>->{<span class="w">AtomicNumber</span>} = <span class="n">0</span><span class="sc">;</span>
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95 82 <span class="i">$This</span>->{<span class="w">XYZ</span>} = <span class="w">Vector::ZeroVector</span><span class="sc">;</span>
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96 83 <span class="s">}</span>
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97 84
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98 85 <span class="c"># Initialize atom properties...</span>
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99 <a name="_InitializeAtomProperties-"></a> 86 <span class="k">sub </span><span class="m">_InitializeAtomProperties</span> <span class="s">{</span>
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100 87 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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101 88
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102 89 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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103 90 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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104 91 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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105 92 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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106 93 <span class="s">}</span>
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107 94 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'AtomSymbol'</span>}<span class="s">)</span> <span class="s">{</span>
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108 95 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Atom object instantiated without setting atom symbol..."</span><span class="sc">;</span>
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109 96 <span class="s">}</span>
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110 97
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111 98 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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112 99 <span class="s">}</span>
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113 100
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114 101 <span class="c"># Initialize class ...</span>
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115 <a name="_InitializeClass-"></a> 102 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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116 103 <span class="c">#Class name...</span>
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117 104 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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118 105
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119 106 <span class="c"># ID to keep track of objects...</span>
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120 107 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span>
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121 108
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122 109 <span class="c"># Load atom class data...</span>
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123 110 <span class="i">_LoadAtomClassData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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124 111 <span class="s">}</span>
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125 112
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126 113 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span>
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127 <a name="SetID-"></a> 114 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span>
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128 115 <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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129 116
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130 117 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span>
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131 118
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132 119 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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133 120 <span class="s">}</span>
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134 121
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135 122 <span class="c"># Setup an explicit SetMolecule method to block setting of ID by AUTOLOAD function...</span>
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136 <a name="SetMolecule-"></a> 123 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span>
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137 124 <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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138 125
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139 126 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMolecule: Molecule property can't be changed: it's used for internal tracking..."</span><span class="sc">;</span>
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140 127
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141 128 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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142 129 <span class="s">}</span>
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143 130
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144 131 <span class="c"># Assign atom to molecule...</span>
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145 <a name="_SetMolecule-"></a> 132 <span class="k">sub </span><span class="m">_SetMolecule</span> <span class="s">{</span>
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146 133 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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147 134
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148 135 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span>
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149 136
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150 137 <span class="c"># Weaken the reference to disable increment of reference count; otherwise,</span>
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151 138 <span class="c"># it it becomes a circular reference and destruction of Molecule object doesn't</span>
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152 139 <span class="c"># get initiated which in turn disables destruction of atom object.</span>
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153 140 <span class="c">#</span>
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154 141 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
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155 142
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156 143 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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157 144 <span class="s">}</span>
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158 145
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159 146 <span class="c"># Setup atom symbol and atomic number for the element...</span>
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160 147 <span class="c">#</span>
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161 148 <span class="c"># Possible atom symbol values:</span>
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162 149 <span class="c"># . An element symbol or some other type of atom: L - Atom list; LP - Lone pair; R# - R group;</span>
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163 150 <span class="c"># A, Q, * - unknown atom; or something else?</span>
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164 151 <span class="c">#</span>
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165 152 <span class="c"># Default mass number corresponds to the most abundant natural isotope unless it's explicity</span>
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166 153 <span class="c"># set using "MassNumber" property.</span>
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167 154 <span class="c">#</span>
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168 <a name="SetAtomSymbol-"></a> 155 <span class="k">sub </span><span class="m">SetAtomSymbol</span> <span class="s">{</span>
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169 156 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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170 157 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
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171 158
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172 159 <span class="i">$This</span>->{<span class="w">AtomSymbol</span>} = <span class="i">$AtomSymbol</span><span class="sc">;</span>
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173 160
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174 161 <span class="i">$AtomicNumber</span> = <span class="i">PeriodicTable::GetElementAtomicNumber</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span>
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175 162 <span class="i">$This</span>->{<span class="w">AtomicNumber</span>} = <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicNumber</span><span class="s">)</span> ? <span class="i">$AtomicNumber</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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176 163
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177 164 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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178 165 <span class="s">}</span>
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179 166
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180 167 <span class="c"># Setup atom symbol and atomic number for the element...</span>
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181 <a name="SetAtomicNumber-"></a> 168 <span class="k">sub </span><span class="m">SetAtomicNumber</span> <span class="s">{</span>
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182 169 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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183 170 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span>
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184 171
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185 172 <span class="i">$AtomSymbol</span> = <span class="i">PeriodicTable::GetElementAtomSymbol</span><span class="s">(</span><span class="i">$AtomicNumber</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="k">defined</span> <span class="i">$AtomSymbol</span><span class="s">)</span> <span class="s">{</span>
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187 174 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicNumber: Didn't set atomic number: Invalid atomic number, $AtomicNumber, specified..."</span><span class="sc">;</span>
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188 175 <span class="k">return</span><span class="sc">;</span>
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189 176 <span class="s">}</span>
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190 177 <span class="i">$This</span>->{<span class="w">AtomicNumber</span>} = <span class="i">$AtomicNumber</span><span class="sc">;</span>
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191 178 <span class="i">$This</span>->{<span class="w">AtomSymbol</span>} = <span class="i">$AtomSymbol</span><span class="sc">;</span>
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192 179
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193 180 <span class="k">return</span> <span class="i">$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"># Set atom as stereo center...</span>
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197 184 <span class="c">#</span>
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198 <a name="SetStereoCenter-"></a> 185 <span class="k">sub </span><span class="m">SetStereoCenter</span> <span class="s">{</span>
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199 186 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StereoCenter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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200 187
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201 188 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'StereoCenter'</span><span class="cm">,</span> <span class="i">$StereoCenter</span><span class="s">)</span><span class="sc">;</span>
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202 189
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203 190 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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204 191 <span class="s">}</span>
|
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205 192
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|
|
206 193 <span class="c"># Is it a stereo center?</span>
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207 194 <span class="c">#</span>
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208 <a name="IsStereoCenter-"></a> 195 <span class="k">sub </span><span class="m">IsStereoCenter</span> <span class="s">{</span>
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209 196 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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210 197 <span class="k">my</span><span class="s">(</span><span class="i">$StereoCenter</span><span class="s">)</span><span class="sc">;</span>
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211 198
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212 199 <span class="i">$StereoCenter</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'StereoCenter'</span><span class="s">)</span><span class="sc">;</span>
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213 200
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214 201 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StereoCenter</span><span class="s">)</span> && <span class="i">$StereoCenter</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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215 202 <span class="s">}</span>
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216 203
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217 204 <span class="c"># Set atom stereochemistry.</span>
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218 205 <span class="c">#</span>
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219 206 <span class="c"># Supported values are: R, S.</span>
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220 207 <span class="c">#</span>
|
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|
221 208 <span class="c"># Notes:</span>
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222 209 <span class="c">#</span>
|
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|
223 210 <span class="c"># . After the ligands around a central stereocenter has been ranked using CIP priority scheme and</span>
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224 211 <span class="c"># the lowest ranked ligand lies behind the center atom, then R and S values correspond to:</span>
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225 212 <span class="c">#</span>
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226 213 <span class="c"># R: Clockwise arrangement of remaining ligands around the central atom going from highest to lowest ranked ligand</span>
|
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227 214 <span class="c"># S: CounterClockwise arrangement of remaining ligands around the central atom going from highest to lowest ranked ligand</span>
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228 215 <span class="c">#</span>
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229 216 <span class="c"># . Assignment of any other arbitray values besides R and S is also allowed; however, a warning is printed.</span>
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230 217 <span class="c">#</span>
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231 <a name="SetStereochemistry-"></a> 218 <span class="k">sub </span><span class="m">SetStereochemistry</span> <span class="s">{</span>
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232 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Stereochemistry</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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233 220
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234 221 <span class="k">if</span> <span class="s">(</span><span class="i">$Stereochemistry</span> !~ <span class="q">/^(R|S)$/i</span><span class="s">)</span> <span class="s">{</span>
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235 222 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetStereochemistry: Assigning non-supported Stereochemistry value of $Stereochemistry. Supported values: R, S..."</span><span class="sc">;</span>
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236 223 <span class="s">}</span>
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237 224
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|
238 225 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'StereoCenter'</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
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239 226 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'Stereochemistry'</span><span class="cm">,</span> <span class="i">$Stereochemistry</span><span class="s">)</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">$This</span><span class="sc">;</span>
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|
|
242 229 <span class="s">}</span>
|
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243 230
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|
244 231 <span class="c"># Setup mass number for atom...</span>
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|
245 <a name="SetMassNumber-"></a> 232 <span class="k">sub </span><span class="m">SetMassNumber</span> <span class="s">{</span>
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|
|
246 233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
247 234 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span>
|
|
|
248 235
|
|
|
249 236 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
250 237 <span class="i">$AtomSymbol</span> = <span class="i">$This</span>->{<span class="w">AtomSymbol</span>}<span class="sc">;</span>
|
|
|
251 238 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
252 239 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMassNumber: Didn't set mass number: Non standard atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol..."</span><span class="sc">;</span>
|
|
|
253 240 <span class="k">return</span><span class="sc">;</span>
|
|
|
254 241 <span class="s">}</span>
|
|
|
255 242 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
256 243 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMassNumber: Unknown mass number, $MassNumber, specified for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope..."</span><span class="sc">;</span>
|
|
|
257 244 <span class="s">}</span>
|
|
|
258 245 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
259 246
|
|
|
260 247 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
261 248 <span class="s">}</span>
|
|
|
262 249
|
|
|
263 250 <span class="c"># Get mass number...</span>
|
|
|
264 251 <span class="c">#</span>
|
|
|
265 <a name="GetMassNumber-"></a> 252 <span class="k">sub </span><span class="m">GetMassNumber</span> <span class="s">{</span>
|
|
|
266 253 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
267 254
|
|
|
268 255 <span class="c"># Is mass number explicity set?</span>
|
|
|
269 256 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
270 257 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
271 258 <span class="s">}</span>
|
|
|
272 259
|
|
|
273 260 <span class="c"># Is it an element symbol?</span>
|
|
|
274 261 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
275 262 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
276 263 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
277 264 <span class="s">}</span>
|
|
|
278 265
|
|
|
279 266 <span class="c"># Return most abundant mass number...</span>
|
|
|
280 267 <span class="k">return</span> <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
281 268 <span class="s">}</span>
|
|
|
282 269
|
|
|
283 270 <span class="c"># Get atomic weight:</span>
|
|
|
284 271 <span class="c"># . Explicitly set by the caller</span>
|
|
|
285 272 <span class="c"># . Using atomic number</span>
|
|
|
286 273 <span class="c">#</span>
|
|
|
287 <a name="GetAtomicWeight-"></a> 274 <span class="k">sub </span><span class="m">GetAtomicWeight</span> <span class="s">{</span>
|
|
|
288 275 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
289 276
|
|
|
290 277 <span class="c"># Is atomic weight explicity set?</span>
|
|
|
291 278 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'AtomicWeight'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
292 279 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'AtomicWeight'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
293 280 <span class="s">}</span>
|
|
|
294 281
|
|
|
295 282 <span class="c"># Is it an element symbol?</span>
|
|
|
296 283 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
297 284 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
298 285 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
299 286 <span class="s">}</span>
|
|
|
300 287
|
|
|
301 288 <span class="c"># Return its atomic weight...</span>
|
|
|
302 289 <span class="k">return</span> <span class="i">PeriodicTable::GetElementAtomicWeight</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
303 290 <span class="s">}</span>
|
|
|
304 291
|
|
|
305 292 <span class="c"># Get exact mass weight:</span>
|
|
|
306 293 <span class="c"># . Explicitly set by the caller</span>
|
|
|
307 294 <span class="c"># . Using atomic number and mass number explicity set by the caller</span>
|
|
|
308 295 <span class="c"># . Using atomic number and most abundant isotope</span>
|
|
|
309 296 <span class="c">#</span>
|
|
|
310 <a name="GetExactMass-"></a> 297 <span class="k">sub </span><span class="m">GetExactMass</span> <span class="s">{</span>
|
|
|
311 298 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
312 299
|
|
|
313 300 <span class="c"># Is exact mass explicity set?</span>
|
|
|
314 301 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ExactMass'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
315 302 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ExactMass'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
316 303 <span class="s">}</span>
|
|
|
317 304
|
|
|
318 305 <span class="c"># Is it an element symbol?</span>
|
|
|
319 306 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
320 307 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
321 308 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
322 309 <span class="s">}</span>
|
|
|
323 310
|
|
|
324 311 <span class="c"># Is mass number explicitly set?</span>
|
|
|
325 312 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
326 313 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
327 314 <span class="k">if</span> <span class="s">(</span><span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
328 315 <span class="k">return</span> <span class="i">PeriodicTable::GetElementNaturalIsotopeMass</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
329 316 <span class="s">}</span>
|
|
|
330 317 <span class="s">}</span>
|
|
|
331 318
|
|
|
332 319 <span class="c"># Return most abundant isotope mass...</span>
|
|
|
333 320 <span class="k">return</span> <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMass</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
334 321 <span class="s">}</span>
|
|
|
335 322
|
|
|
336 323 <span class="c"># Get formal charge:</span>
|
|
|
337 324 <span class="c"># . Explicitly set by the caller</span>
|
|
|
338 325 <span class="c"># . Or return zero insetad of undef</span>
|
|
|
339 326 <span class="c">#</span>
|
|
|
340 <a name="GetFormalCharge-"></a> 327 <span class="k">sub </span><span class="m">GetFormalCharge</span> <span class="s">{</span>
|
|
|
341 328 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
342 329 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
343 330
|
|
|
344 331 <span class="i">$FormalCharge</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
345 332 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
346 333 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
347 334 <span class="s">}</span>
|
|
|
348 335
|
|
|
349 336 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> ? <span class="i">$FormalCharge</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
350 337 <span class="s">}</span>
|
|
|
351 338
|
|
|
352 339 <span class="c"># Get spin multiplicity:</span>
|
|
|
353 340 <span class="c"># . Explicitly set by the caller</span>
|
|
|
354 341 <span class="c"># . From FreeRadicalElectrons value explicitly set by the caller</span>
|
|
|
355 342 <span class="c"># . Or return zero insetad of undef</span>
|
|
|
356 343 <span class="c">#</span>
|
|
|
357 <a name="GetSpinMultiplicity-"></a> 344 <span class="k">sub </span><span class="m">GetSpinMultiplicity</span> <span class="s">{</span>
|
|
|
358 345 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
359 346 <span class="k">my</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
360 347
|
|
|
361 348 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
362 349 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
363 350 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
364 351 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span> ? <span class="i">$SpinMultiplicity</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
365 352 <span class="s">}</span>
|
|
|
366 353
|
|
|
367 354 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
368 355 <span class="k">my</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span><span class="sc">;</span>
|
|
|
369 356 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
370 357
|
|
|
371 358 <span class="j">SPINMULTIPLICITY:</span> <span class="s">{</span>
|
|
|
372 359 <span class="k">if</span> <span class="s">(</span><span class="i">$FreeRadicalElectrons</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> <span class="i">$SpinMultiplicity</span> = <span class="n">2</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span>
|
|
|
373 360 <span class="k">if</span> <span class="s">(</span><span class="i">$FreeRadicalElectrons</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> <span class="i">$SpinMultiplicity</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span>
|
|
|
374 361 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetSpinMultiplicity: It's not possible to determine spin multiplicity from the specified free radical electrons value, $FreeRadicalElectrons. It has been set to 0..."</span><span class="sc">;</span>
|
|
|
375 362 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
376 363 <span class="s">}</span>
|
|
|
377 364 <span class="s">}</span>
|
|
|
378 365
|
|
|
379 366 <span class="k">return</span> <span class="i">$SpinMultiplicity</span><span class="sc">;</span>
|
|
|
380 367 <span class="s">}</span>
|
|
|
381 368
|
|
|
382 369 <span class="c"># Get number of free radical electrons:</span>
|
|
|
383 370 <span class="c"># . Explicitly set by the caller</span>
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|
384 371 <span class="c"># . From SpinMultiplicity value explicitly set by the caller</span>
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|
385 372 <span class="c"># . Or return zero insetad of undef</span>
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|
386 373 <span class="c">#</span>
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|
387 374 <span class="c"># Notes:</span>
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|
388 375 <span class="c"># . For atoms with explicit assignment of SpinMultiplicity property values corresponding to</span>
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|
389 376 <span class="c"># Singlet (two unpaired electrons corresponding to one spin state), Doublet (free radical; an unpaired</span>
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390 377 <span class="c"># electron corresponding to two spin states), and Triplet (two unparied electrons corresponding to</span>
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391 378 <span class="c"># three spin states; divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:</span>
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392 379 <span class="c">#</span>
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393 380 <span class="c"># SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1</span>
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|
394 381 <span class="c"># SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2</span>
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395 382 <span class="c">#</span>
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396 <a name="GetFreeRadicalElectrons-"></a> 383 <span class="k">sub </span><span class="m">GetFreeRadicalElectrons</span> <span class="s">{</span>
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397 384 <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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398 385 <span class="k">my</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span><span class="sc">;</span>
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399 386
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400 387 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span>
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401 388
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402 389 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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403 390 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="sc">;</span>
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404 391 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span> ? <span class="i">$FreeRadicalElectrons</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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405 392 <span class="s">}</span>
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406 393
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407 394 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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408 395 <span class="k">my</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span>
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409 396 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span>
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410 397
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411 398 <span class="j">SPINMULTIPLICITY:</span> <span class="s">{</span>
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412 399 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">2</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span>
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413 400 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span>
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414 401 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">2</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span>
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415 402 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetFreeRadicalElectrons: It's not possible to determine free radical electrons from the specified spin multiplicity value, $FreeRadicalElectrons. It has been set to 0..."</span><span class="sc">;</span>
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416 403 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span>
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|
417 404 <span class="s">}</span>
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|
|
418 405 <span class="s">}</span>
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419 406
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|
|
420 407 <span class="k">return</span> <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span>
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|
|
421 408 <span class="s">}</span>
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422 409
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423 410 <span class="c"># Set atom coordinates using:</span>
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|
424 411 <span class="c"># . An array reference with three values</span>
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|
425 412 <span class="c"># . An array containg three values</span>
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|
426 413 <span class="c"># . A 3D vector</span>
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427 414 <span class="c">#</span>
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428 <a name="SetXYZ-"></a> 415 <span class="k">sub </span><span class="m">SetXYZ</span> <span class="s">{</span>
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|
429 416 <span class="k">my</span><span class="s">(</span><span class="i">$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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430 417
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|
431 418 <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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|
432 419 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetXYZ: No values specified..."</span><span class="sc">;</span>
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|
433 420 <span class="k">return</span><span class="sc">;</span>
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|
|
434 421 <span class="s">}</span>
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|
435 422
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|
436 423 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetXYZ</span><span class="s">(</span><span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
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|
|
437 424 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
438 425 <span class="s">}</span>
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|
439 426
|
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|
440 427 <span class="c"># Set X value...</span>
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|
441 <a name="SetX-"></a> 428 <span class="k">sub </span><span class="m">SetX</span> <span class="s">{</span>
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|
442 429 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
443 430
|
|
|
444 431 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span>
|
|
|
445 432 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetX: Undefined X value..."</span><span class="sc">;</span>
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|
|
446 433 <span class="k">return</span><span class="sc">;</span>
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|
|
447 434 <span class="s">}</span>
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|
|
448 435 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetX</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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|
|
449 436 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
450 437 <span class="s">}</span>
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|
|
451 438
|
|
|
452 439 <span class="c"># Set Y value...</span>
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|
453 <a name="SetY-"></a> 440 <span class="k">sub </span><span class="m">SetY</span> <span class="s">{</span>
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|
454 441 <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>
|
|
|
455 442
|
|
|
456 443 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span>
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|
|
457 444 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetY: Undefined Y value..."</span><span class="sc">;</span>
|
|
|
458 445 <span class="k">return</span><span class="sc">;</span>
|
|
|
459 446 <span class="s">}</span>
|
|
|
460 447 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetY</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
461 448 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
462 449 <span class="s">}</span>
|
|
|
463 450
|
|
|
464 451 <span class="c"># Set Z value...</span>
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|
|
465 <a name="SetZ-"></a> 452 <span class="k">sub </span><span class="m">SetZ</span> <span class="s">{</span>
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|
|
466 453 <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>
|
|
|
467 454
|
|
|
468 455 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span>
|
|
|
469 456 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetZ: Undefined Z value..."</span><span class="sc">;</span>
|
|
|
470 457 <span class="k">return</span><span class="sc">;</span>
|
|
|
471 458 <span class="s">}</span>
|
|
|
472 459 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->SetZ</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
473 460 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
474 461 <span class="s">}</span>
|
|
|
475 462
|
|
|
476 463 <span class="c"># Return XYZ as:</span>
|
|
|
477 464 <span class="c"># . Reference to an array</span>
|
|
|
478 465 <span class="c"># . An array</span>
|
|
|
479 466 <span class="c">#</span>
|
|
|
480 <a name="GetXYZ-"></a> 467 <span class="k">sub </span><span class="m">GetXYZ</span> <span class="s">{</span>
|
|
|
481 468 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
482 469
|
|
|
483 470 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetXYZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
484 471 <span class="s">}</span>
|
|
|
485 472
|
|
|
486 473 <span class="c"># Return XYZ as a vector object...</span>
|
|
|
487 474 <span class="c">#</span>
|
|
|
488 <a name="GetXYZVector-"></a> 475 <span class="k">sub </span><span class="m">GetXYZVector</span> <span class="s">{</span>
|
|
|
489 476 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
490 477
|
|
|
491 478 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="sc">;</span>
|
|
|
492 479 <span class="s">}</span>
|
|
|
493 480
|
|
|
494 481 <span class="c"># Get X value...</span>
|
|
|
495 <a name="GetX-"></a> 482 <span class="k">sub </span><span class="m">GetX</span> <span class="s">{</span>
|
|
|
496 483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
497 484
|
|
|
498 485 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetX</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
499 486 <span class="s">}</span>
|
|
|
500 487
|
|
|
501 488 <span class="c"># Get Y value...</span>
|
|
|
502 <a name="GetY-"></a> 489 <span class="k">sub </span><span class="m">GetY</span> <span class="s">{</span>
|
|
|
503 490 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
504 491
|
|
|
505 492 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetY</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
506 493 <span class="s">}</span>
|
|
|
507 494
|
|
|
508 495 <span class="c"># Get Z value...</span>
|
|
|
509 <a name="GetZ-"></a> 496 <span class="k">sub </span><span class="m">GetZ</span> <span class="s">{</span>
|
|
|
510 497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
511 498
|
|
|
512 499 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
513 500 <span class="s">}</span>
|
|
|
514 501
|
|
|
515 502 <span class="c"># Delete atom...</span>
|
|
|
516 <a name="DeleteAtom-"></a> 503 <span class="k">sub </span><span class="m">DeleteAtom</span> <span class="s">{</span>
|
|
|
517 504 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
518 505
|
|
|
519 506 <span class="c"># Is this atom in a molecule?</span>
|
|
|
520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
521 508 <span class="c"># Nothing to do...</span>
|
|
|
522 509 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
523 510 <span class="s">}</span>
|
|
|
524 511 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
525 512
|
|
|
526 513 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
527 514 <span class="s">}</span>
|
|
|
528 515
|
|
|
529 516 <span class="c"># Get atom neighbor objects as array. In scalar conetxt, return number of neighbors...</span>
|
|
|
530 <a name="GetNeighbors-"></a> 517 <span class="k">sub </span><span class="m">GetNeighbors</span> <span class="s">{</span>
|
|
|
531 518 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
532 519
|
|
|
533 520 <span class="c"># Is this atom in a molecule?</span>
|
|
|
534 521 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
535 522 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
536 523 <span class="s">}</span>
|
|
|
537 524 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
538 525
|
|
|
539 526 <span class="k">if</span> <span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span>
|
|
|
540 527 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
541 528 <span class="s">}</span>
|
|
|
542 529 <span class="k">else</span> <span class="s">{</span>
|
|
|
543 530 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
544 531 <span class="s">}</span>
|
|
|
545 532 <span class="s">}</span>
|
|
|
546 533
|
|
|
547 534 <span class="c"># Get atom neighbor objects as array. In scalar conetxt, return number of neighbors...</span>
|
|
|
548 <a name="_GetAtomNeighbors-"></a> 535 <span class="k">sub </span><span class="m">_GetAtomNeighbors</span> <span class="s">{</span>
|
|
|
549 536 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
550 537 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
551 538
|
|
|
552 539 <span class="k">if</span> <span class="s">(</span>!<span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span>
|
|
|
553 540 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
554 541 <span class="s">}</span>
|
|
|
555 542
|
|
|
556 543 <span class="c"># Setup a map for neigbhors to exclude...</span>
|
|
|
557 544 <span class="k">my</span><span class="s">(</span><span class="i">$ExcludeNeighbor</span><span class="cm">,</span> <span class="i">$ExcludeNeighborID</span><span class="cm">,</span> <span class="i">%ExcludeNeighborsIDsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
558 545
|
|
|
559 546 <span class="i">%ExcludeNeighborsIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
560 547 <span class="k">for</span> <span class="i">$ExcludeNeighbor</span> <span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span>
|
|
|
561 548 <span class="i">$ExcludeNeighborID</span> = <span class="i">$ExcludeNeighbor</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
562 549 <span class="i">$ExcludeNeighborsIDsMap</span>{<span class="i">$ExcludeNeighborID</span>} = <span class="i">$ExcludeNeighborID</span><span class="sc">;</span>
|
|
|
563 550 <span class="s">}</span>
|
|
|
564 551
|
|
|
565 552 <span class="c"># Generate a filtered neighbors list...</span>
|
|
|
566 553 <span class="k">my</span><span class="s">(</span><span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">$NeighborID</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
567 554 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
568 555 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
569 556 <span class="i">$NeighborID</span> = <span class="i">$Neighbor</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
570 557 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ExcludeNeighborsIDsMap</span>{<span class="i">$NeighborID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
571 558 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
|
|
|
572 559 <span class="s">}</span>
|
|
|
573 560 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="sc">;</span>
|
|
|
574 561 <span class="s">}</span>
|
|
|
575 562
|
|
|
576 563 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtomNeighbors</span><span class="sc">;</span>
|
|
|
577 564 <span class="s">}</span>
|
|
|
578 565
|
|
|
579 566 <span class="c"># Get specific atom neighbor objects as array. In scalar conetxt, return number of neighbors.</span>
|
|
|
580 567 <span class="c">#</span>
|
|
|
581 568 <span class="c"># Notes:</span>
|
|
|
582 569 <span class="c"># . AtomSpecification correspond to any valid AtomicInvariant based atomic specifications</span>
|
|
|
583 570 <span class="c"># as implemented in DoesAtomNeighborhoodMatch method.</span>
|
|
|
584 571 <span class="c"># . Multiple atom specifications can be used in a string delimited by comma.</span>
|
|
|
585 572 <span class="c">#</span>
|
|
|
586 <a name="GetNeighborsUsingAtomSpecification-"></a> 573 <span class="k">sub </span><span class="m">GetNeighborsUsingAtomSpecification</span> <span class="s">{</span>
|
|
|
587 574 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomSpecification</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
588 575 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
589 576
|
|
|
590 577 <span class="i">@AtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
591 578 <span class="i">@AtomNeighbors</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
592 579
|
|
|
593 580 <span class="c"># Does atom has any neighbors and do they need to be filtered?</span>
|
|
|
594 581 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">@AtomNeighbors</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="s">)</span> && <span class="i">$AtomSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
595 582 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@AtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@AtomNeighbors</span><span class="sc">;</span>
|
|
|
596 583 <span class="s">}</span>
|
|
|
597 584
|
|
|
598 585 <span class="c"># Filter neighbors using atom specification...</span>
|
|
|
599 586 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
600 587
|
|
|
601 588 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
602 589 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span> <span class="s">{</span>
|
|
|
603 590 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomNeighbor</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
604 591 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
|
|
|
605 592 <span class="s">}</span>
|
|
|
606 593 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$AtomNeighbor</span><span class="sc">;</span>
|
|
|
607 594 <span class="s">}</span>
|
|
|
608 595
|
|
|
609 596 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtomNeighbors</span><span class="sc">;</span>
|
|
|
610 597 <span class="s">}</span>
|
|
|
611 598
|
|
|
612 599
|
|
|
613 600 <span class="c"># Get non-hydrogen atom neighbor objects as array. In scalar context, return number of neighbors...</span>
|
|
|
614 <a name="GetHeavyAtomNeighbors-"></a> 601 <span class="k">sub </span><span class="m">GetHeavyAtomNeighbors</span> <span class="s">{</span>
|
|
|
615 602 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
616 603
|
|
|
617 604 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
618 605 <span class="s">}</span>
|
|
|
619 606
|
|
|
620 607 <span class="c"># Get non-hydrogen atom neighbor objects as array. In scalar context, return number of neighbors...</span>
|
|
|
621 <a name="GetNonHydrogenAtomNeighbors-"></a> 608 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighbors</span> <span class="s">{</span>
|
|
|
622 609 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
623 610
|
|
|
624 611 <span class="c"># Is this atom in a molecule?</span>
|
|
|
625 612 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
626 613 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
627 614 <span class="s">}</span>
|
|
|
628 615 <span class="k">my</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
629 616
|
|
|
630 617 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFilteredAtomNeighbors</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
|
|
|
631 618 <span class="s">}</span>
|
|
|
632 619
|
|
|
633 620 <span class="c"># Get hydrogen atom neighbor objects as array. In scalar context, return numbe of neighbors...</span>
|
|
|
634 <a name="GetHydrogenAtomNeighbors-"></a> 621 <span class="k">sub </span><span class="m">GetHydrogenAtomNeighbors</span> <span class="s">{</span>
|
|
|
635 622 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
636 623
|
|
|
637 624 <span class="c"># Is this atom in a molecule?</span>
|
|
|
638 625 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
639 626 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
640 627 <span class="s">}</span>
|
|
|
641 628 <span class="k">my</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
642 629
|
|
|
643 630 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFilteredAtomNeighbors</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
|
|
|
644 631 <span class="s">}</span>
|
|
|
645 632
|
|
|
646 633 <span class="c"># Get non-hydrogen neighbor of hydrogen atom...</span>
|
|
|
647 634 <span class="c">#</span>
|
|
|
648 <a name="GetNonHydrogenNeighborOfHydrogenAtom-"></a> 635 <span class="k">sub </span><span class="m">GetNonHydrogenNeighborOfHydrogenAtom</span> <span class="s">{</span>
|
|
|
649 636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
650 637
|
|
|
651 638 <span class="c"># Is it Hydrogen?</span>
|
|
|
652 639 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
653 640 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
654 641 <span class="s">}</span>
|
|
|
655 642 <span class="k">my</span><span class="s">(</span><span class="i">@Neighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
656 643
|
|
|
657 644 <span class="i">@Neighbors</span> = <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
658 645
|
|
|
659 646 <span class="k">return</span> <span class="s">(</span><span class="i">@Neighbors</span> == <span class="n">1</span><span class="s">)</span> ? <span class="i">$Neighbors</span>[<span class="n">0</span>] <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
660 647 <span class="s">}</span>
|
|
|
661 648
|
|
|
662 649 <span class="c"># Get filtered atom atom neighbors</span>
|
|
|
663 <a name="_GetFilteredAtomNeighbors-"></a> 650 <span class="k">sub </span><span class="m">_GetFilteredAtomNeighbors</span> <span class="s">{</span>
|
|
|
664 651 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
665 652
|
|
|
666 653 <span class="c"># Check flags...</span>
|
|
|
667 654 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
668 655 <span class="i">$NonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
669 656 <span class="s">}</span>
|
|
|
670 657 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
671 658 <span class="i">$HydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
672 659 <span class="s">}</span>
|
|
|
673 660 <span class="k">my</span><span class="s">(</span><span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
674 661
|
|
|
675 662 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
676 663 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
677 664 <span class="k">if</span> <span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span> && <span class="i">$Neighbor</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
678 665 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
|
|
|
679 666 <span class="s">}</span>
|
|
|
680 667 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenAtomsOnly</span> && <span class="s">(</span>!<span class="i">$Neighbor</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
681 668 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
|
|
|
682 669 <span class="s">}</span>
|
|
|
683 670 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="sc">;</span>
|
|
|
684 671 <span class="s">}</span>
|
|
|
685 672
|
|
|
686 673 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtomNeighbors</span><span class="sc">;</span>
|
|
|
687 674 <span class="s">}</span>
|
|
|
688 675
|
|
|
689 676 <span class="c"># Get number of neighbors...</span>
|
|
|
690 677 <span class="c">#</span>
|
|
|
691 <a name="GetNumOfNeighbors-"></a> 678 <span class="k">sub </span><span class="m">GetNumOfNeighbors</span> <span class="s">{</span>
|
|
|
692 679 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
693 680 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
694 681
|
|
|
695 682 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
696 683
|
|
|
697 684 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
698 685 <span class="s">}</span>
|
|
|
699 686
|
|
|
700 687 <span class="c"># Get number of neighbors which are non-hydrogen atoms...</span>
|
|
|
701 <a name="GetNumOfHeavyAtomNeighbors-"></a> 688 <span class="k">sub </span><span class="m">GetNumOfHeavyAtomNeighbors</span> <span class="s">{</span>
|
|
|
702 689 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
703 690
|
|
|
704 691 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
705 692 <span class="s">}</span>
|
|
|
706 693
|
|
|
707 694 <span class="c"># Get number of neighbors which are non-hydrogen atoms...</span>
|
|
|
708 <a name="GetNumOfNonHydrogenAtomNeighbors-"></a> 695 <span class="k">sub </span><span class="m">GetNumOfNonHydrogenAtomNeighbors</span> <span class="s">{</span>
|
|
|
709 696 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
710 697 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
711 698
|
|
|
712 699 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
713 700
|
|
|
714 701 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
715 702 <span class="s">}</span>
|
|
|
716 703
|
|
|
717 704 <span class="c"># Get number of neighbors which are hydrogen atoms...</span>
|
|
|
718 <a name="GetNumOfHydrogenAtomNeighbors-"></a> 705 <span class="k">sub </span><span class="m">GetNumOfHydrogenAtomNeighbors</span> <span class="s">{</span>
|
|
|
719 706 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
720 707 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
721 708
|
|
|
722 709 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
723 710
|
|
|
724 711 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
725 712 <span class="s">}</span>
|
|
|
726 713
|
|
|
727 714 <span class="c"># Get bond objects as array. In scalar context, return number of bonds...</span>
|
|
|
728 <a name="GetBonds-"></a> 715 <span class="k">sub </span><span class="m">GetBonds</span> <span class="s">{</span>
|
|
|
729 716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
730 717
|
|
|
731 718 <span class="c"># Is this atom in a molecule?</span>
|
|
|
732 719 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
733 720 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
734 721 <span class="s">}</span>
|
|
|
735 722 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
736 723
|
|
|
737 724 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomBonds</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
738 725 <span class="s">}</span>
|
|
|
739 726
|
|
|
740 727 <span class="c"># Get bond to specified atom...</span>
|
|
|
741 <a name="GetBondToAtom-"></a> 728 <span class="k">sub </span><span class="m">GetBondToAtom</span> <span class="s">{</span>
|
|
|
742 729 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
743 730
|
|
|
744 731 <span class="c"># Is this atom in a molecule?</span>
|
|
|
745 732 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
746 733 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
747 734 <span class="s">}</span>
|
|
|
748 735 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
749 736
|
|
|
750 737 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondToAtom</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span><span class="sc">;</span>
|
|
|
751 738 <span class="s">}</span>
|
|
|
752 739
|
|
|
753 740 <span class="c"># It it bonded to a specified atom?</span>
|
|
|
754 <a name="IsBondedToAtom-"></a> 741 <span class="k">sub </span><span class="m">IsBondedToAtom</span> <span class="s">{</span>
|
|
|
755 742 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
756 743
|
|
|
757 744 <span class="c"># Is this atom in a molecule?</span>
|
|
|
758 745 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
759 746 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
760 747 <span class="s">}</span>
|
|
|
761 748 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
762 749
|
|
|
763 750 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondedToAtom</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span><span class="sc">;</span>
|
|
|
764 751 <span class="s">}</span>
|
|
|
765 752
|
|
|
766 753 <span class="c"># Get bond objects to non-hydrogen atoms as array. In scalar context, return number of bonds...</span>
|
|
|
767 <a name="GetBondsToHeavyAtoms-"></a> 754 <span class="k">sub </span><span class="m">GetBondsToHeavyAtoms</span> <span class="s">{</span>
|
|
|
768 755 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
769 756
|
|
|
770 757 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
771 758 <span class="s">}</span>
|
|
|
772 759
|
|
|
773 760 <span class="c"># Get bond objects to non-hydrogen atoms as array. In scalar context, return number of bonds...</span>
|
|
|
774 <a name="GetBondsToNonHydrogenAtoms-"></a> 761 <span class="k">sub </span><span class="m">GetBondsToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
775 762 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
776 763
|
|
|
777 764 <span class="c"># Is this atom in a molecule?</span>
|
|
|
778 765 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
779 766 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
780 767 <span class="s">}</span>
|
|
|
781 768 <span class="k">my</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
782 769
|
|
|
783 770 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFilteredBonds</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
|
|
|
784 771 <span class="s">}</span>
|
|
|
785 772
|
|
|
786 773 <span class="c"># Get bond objects to hydrogen atoms as array. In scalar context, return number of bonds...</span>
|
|
|
787 <a name="GetBondsToHydrogenAtoms-"></a> 774 <span class="k">sub </span><span class="m">GetBondsToHydrogenAtoms</span> <span class="s">{</span>
|
|
|
788 775 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
789 776
|
|
|
790 777 <span class="c"># Is this atom in a molecule?</span>
|
|
|
791 778 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
792 779 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
793 780 <span class="s">}</span>
|
|
|
794 781 <span class="k">my</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
795 782
|
|
|
796 783 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFilteredBonds</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
|
|
|
797 784 <span class="s">}</span>
|
|
|
798 785
|
|
|
799 786 <span class="c"># Get filtered bonds...</span>
|
|
|
800 <a name="_GetFilteredBonds-"></a> 787 <span class="k">sub </span><span class="m">_GetFilteredBonds</span> <span class="s">{</span>
|
|
|
801 788 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
802 789
|
|
|
803 790 <span class="c"># Check flags...</span>
|
|
|
804 791 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
805 792 <span class="i">$BondsToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
806 793 <span class="s">}</span>
|
|
|
807 794 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
808 795 <span class="i">$BondsToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
809 796 <span class="s">}</span>
|
|
|
810 797
|
|
|
811 798 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">@FilteredBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
812 799
|
|
|
813 800 <span class="i">@FilteredBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
814 801 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
815 802 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
816 803 <span class="k">if</span> <span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span> && <span class="i">$BondedAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
817 804 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
818 805 <span class="s">}</span>
|
|
|
819 806 <span class="k">if</span> <span class="s">(</span><span class="i">$BondsToHydrogenAtomsOnly</span> && <span class="s">(</span>!<span class="i">$BondedAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
820 807 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
821 808 <span class="s">}</span>
|
|
|
822 809 <span class="k">push</span> <span class="i">@FilteredBonds</span><span class="cm">,</span> <span class="i">$Bond</span><span class="sc">;</span>
|
|
|
823 810 <span class="s">}</span>
|
|
|
824 811
|
|
|
825 812 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredBonds</span> <span class="co">:</span> <span class="s">(</span><span class="k">scalar</span> <span class="i">@FilteredBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
826 813 <span class="s">}</span>
|
|
|
827 814
|
|
|
828 815 <span class="c"># Get number of bonds...</span>
|
|
|
829 816 <span class="c">#</span>
|
|
|
830 <a name="GetNumOfBonds-"></a> 817 <span class="k">sub </span><span class="m">GetNumOfBonds</span> <span class="s">{</span>
|
|
|
831 818 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
832 819 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
833 820
|
|
|
834 821 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
835 822
|
|
|
836 823 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
837 824 <span class="s">}</span>
|
|
|
838 825
|
|
|
839 826 <span class="c"># Get number of bonds to non-hydrogen atoms...</span>
|
|
|
840 <a name="GetNumOfBondsToHeavyAtoms-"></a> 827 <span class="k">sub </span><span class="m">GetNumOfBondsToHeavyAtoms</span> <span class="s">{</span>
|
|
|
841 828 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
842 829
|
|
|
843 830 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
844 831 <span class="s">}</span>
|
|
|
845 832
|
|
|
846 833 <span class="c"># Get number of bonds to non-hydrogen atoms...</span>
|
|
|
847 <a name="GetNumOfBondsToNonHydrogenAtoms-"></a> 834 <span class="k">sub </span><span class="m">GetNumOfBondsToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
848 835 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
849 836 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
850 837
|
|
|
851 838 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
852 839
|
|
|
853 840 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
854 841 <span class="s">}</span>
|
|
|
855 842
|
|
|
856 843 <span class="c"># Get number of single bonds to heavy atoms...</span>
|
|
|
857 <a name="GetNumOfSingleBondsToHeavyAtoms-"></a> 844 <span class="k">sub </span><span class="m">GetNumOfSingleBondsToHeavyAtoms</span> <span class="s">{</span>
|
|
|
858 845 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
859 846
|
|
|
860 847 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
861 848 <span class="s">}</span>
|
|
|
862 849
|
|
|
863 850 <span class="c"># Get number of single bonds to non-hydrogen atoms...</span>
|
|
|
864 <a name="GetNumOfSingleBondsToNonHydrogenAtoms-"></a> 851 <span class="k">sub </span><span class="m">GetNumOfSingleBondsToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
865 852 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
866 853
|
|
|
867 854 <span class="c"># Is this atom in a molecule?</span>
|
|
|
868 855 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
869 856 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
870 857 <span class="s">}</span>
|
|
|
871 858 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
872 859 <span class="s">}</span>
|
|
|
873 860
|
|
|
874 861 <span class="c"># Get number of double bonds to heavy atoms...</span>
|
|
|
875 <a name="GetNumOfDoubleBondsToHeavyAtoms-"></a> 862 <span class="k">sub </span><span class="m">GetNumOfDoubleBondsToHeavyAtoms</span> <span class="s">{</span>
|
|
|
876 863 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
877 864
|
|
|
878 865 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
879 866 <span class="s">}</span>
|
|
|
880 867
|
|
|
881 868 <span class="c"># Get number of double bonds to non-hydrogen atoms...</span>
|
|
|
882 <a name="GetNumOfDoubleBondsToNonHydrogenAtoms-"></a> 869 <span class="k">sub </span><span class="m">GetNumOfDoubleBondsToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
883 870 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
884 871
|
|
|
885 872 <span class="c"># Is this atom in a molecule?</span>
|
|
|
886 873 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
887 874 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
888 875 <span class="s">}</span>
|
|
|
889 876 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
890 877 <span class="s">}</span>
|
|
|
891 878
|
|
|
892 879 <span class="c"># Get number of triple bonds to heavy atoms...</span>
|
|
|
893 <a name="GetNumOfTripleBondsToHeavyAtoms-"></a> 880 <span class="k">sub </span><span class="m">GetNumOfTripleBondsToHeavyAtoms</span> <span class="s">{</span>
|
|
|
894 881 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
895 882
|
|
|
896 883 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfTripleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
897 884 <span class="s">}</span>
|
|
|
898 885
|
|
|
899 886 <span class="c"># Get number of triple bonds to non-hydrogen atoms...</span>
|
|
|
900 <a name="GetNumOfTripleBondsToNonHydrogenAtoms-"></a> 887 <span class="k">sub </span><span class="m">GetNumOfTripleBondsToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
901 888 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
902 889
|
|
|
903 890 <span class="c"># Is this atom in a molecule?</span>
|
|
|
904 891 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
905 892 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
906 893 <span class="s">}</span>
|
|
|
907 894 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">3</span><span class="s">)</span><span class="sc">;</span>
|
|
|
908 895 <span class="s">}</span>
|
|
|
909 896
|
|
|
910 897 <span class="c"># Get number of bonds of specified bond order to non-hydrogen atoms...</span>
|
|
|
911 <a name="_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms-"></a> 898 <span class="k">sub </span><span class="m">_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
912 899 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$SpecifiedBondOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
913 900 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
914 901
|
|
|
915 902 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
916 903 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
917 904 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
918 905 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
919 906 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedBondOrder</span> == <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span>
|
|
|
920 907 <span class="i">$NumOfBonds</span>++<span class="sc">;</span>
|
|
|
921 908 <span class="s">}</span>
|
|
|
922 909 <span class="s">}</span>
|
|
|
923 910 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span>
|
|
|
924 911 <span class="s">}</span>
|
|
|
925 912
|
|
|
926 913 <span class="c"># Get number of aromatic bonds to heavy atoms...</span>
|
|
|
927 <a name="GetNumOfAromaticBondsToHeavyAtoms-"></a> 914 <span class="k">sub </span><span class="m">GetNumOfAromaticBondsToHeavyAtoms</span> <span class="s">{</span>
|
|
|
928 915 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
929 916
|
|
|
930 917 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
931 918 <span class="s">}</span>
|
|
|
932 919
|
|
|
933 920 <span class="c"># Get number of aromatic bonds to non-hydrogen atoms...</span>
|
|
|
934 <a name="GetNumOfAromaticBondsToNonHydrogenAtoms-"></a> 921 <span class="k">sub </span><span class="m">GetNumOfAromaticBondsToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
935 922 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
936 923 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
937 924
|
|
|
938 925 <span class="c"># Is this atom in a molecule?</span>
|
|
|
939 926 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
940 927 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
941 928 <span class="s">}</span>
|
|
|
942 929
|
|
|
943 930 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
944 931 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
945 932 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
946 933 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfBonds</span>++<span class="sc">;</span> <span class="s">}</span>
|
|
|
947 934 <span class="s">}</span>
|
|
|
948 935 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span>
|
|
|
949 936 <span class="s">}</span>
|
|
|
950 937
|
|
|
951 938 <span class="c"># Get number of different bond types to non-hydrogen atoms...</span>
|
|
|
952 939 <span class="c">#</span>
|
|
|
953 <a name="GetNumOfBondTypesToHeavyAtoms-"></a> 940 <span class="k">sub </span><span class="m">GetNumOfBondTypesToHeavyAtoms</span> <span class="s">{</span>
|
|
|
954 941 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CountAromaticBonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
955 942
|
|
|
956 943 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfBondTypesToNonHydrogenAtoms</span><span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
957 944 <span class="s">}</span>
|
|
|
958 945
|
|
|
959 946 <span class="c"># Get number of single, double, triple, and aromatic bonds from an atom to all other</span>
|
|
|
960 947 <span class="c"># non-hydrogen atoms. Value of CountAtomaticBonds parameter controls whether</span>
|
|
|
961 948 <span class="c"># number of aromatic bonds is returned; default is not to count aromatic bonds. During</span>
|
|
|
962 949 <span class="c"># counting of aromatic bonds, the bond marked aromatic is not included in the count</span>
|
|
|
963 950 <span class="c"># of other bond types.</span>
|
|
|
964 951 <span class="c">#</span>
|
|
|
965 <a name="GetNumOfBondTypesToNonHydrogenAtoms-"></a> 952 <span class="k">sub </span><span class="m">GetNumOfBondTypesToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
966 953 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CountAromaticBonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
967 954 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="cm">,</span> <span class="i">$None</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
968 955
|
|
|
969 956 <span class="i">$CountAromaticBonds</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span> ? <span class="i">$CountAromaticBonds</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
970 957
|
|
|
971 958 <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
|
|
|
972 959 <span class="i">$NumOfAromaticBonds</span> = <span class="i">$CountAromaticBonds</span> ? <span class="n">0</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
973 960
|
|
|
974 961 <span class="c"># Is this atom in a molecule?</span>
|
|
|
975 962 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
976 963 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
977 964 <span class="s">}</span>
|
|
|
978 965
|
|
|
979 966 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
980 967
|
|
|
981 968 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
982 969 <span class="j">BONDTYPE:</span> <span class="s">{</span>
|
|
|
983 970 <span class="k">if</span> <span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
984 971 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfAromaticBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
985 972 <span class="s">}</span>
|
|
|
986 973 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsSingle</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfSingleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
987 974 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsDouble</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfDoubleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
988 975 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsTriple</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfTripleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
989 976 <span class="i">$None</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
990 977 <span class="s">}</span>
|
|
|
991 978 <span class="s">}</span>
|
|
|
992 979 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
993 980 <span class="s">}</span>
|
|
|
994 981
|
|
|
995 982 <span class="c"># Get number of sigma and pi bonds to heavy atoms...</span>
|
|
|
996 983 <span class="c">#</span>
|
|
|
997 <a name="GetNumOfSigmaAndPiBondsToHeavyAtoms-"></a> 984 <span class="k">sub </span><span class="m">GetNumOfSigmaAndPiBondsToHeavyAtoms</span> <span class="s">{</span>
|
|
|
998 985 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
999 986
|
|
|
1000 987 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1001 988 <span class="s">}</span>
|
|
|
1002 989
|
|
|
1003 990 <span class="c"># Get number of sigma and pi bonds from an atom to all other non-hydrogen atoms.</span>
|
|
|
1004 991 <span class="c"># Sigma and pi bonds are counted using the following methodology: a single bond</span>
|
|
|
1005 992 <span class="c"># correspond to one sigma bond; a double bond contributes one to sigma bond count</span>
|
|
|
1006 993 <span class="c"># and one to pi bond count; a triple bond contributes one to sigma bond count and</span>
|
|
|
1007 994 <span class="c"># two to pi bond count.</span>
|
|
|
1008 995 <span class="c">#</span>
|
|
|
1009 <a name="GetNumOfSigmaAndPiBondsToNonHydrogenAtoms-"></a> 996 <span class="k">sub </span><span class="m">GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
1010 997 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1011 998 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfSigmaBonds</span><span class="cm">,</span> <span class="i">$NumOfPiBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1012 999
|
|
|
1013 1000 <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetNumOfBondTypesToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1014 1001
|
|
|
1015 1002 <span class="i">$NumOfSigmaBonds</span> = <span class="i">$NumOfSingleBonds</span> + <span class="i">$NumOfDoubleBonds</span> + <span class="i">$NumOfTripleBonds</span><span class="sc">;</span>
|
|
|
1016 1003 <span class="i">$NumOfPiBonds</span> = <span class="i">$NumOfDoubleBonds</span> + <span class="n">2</span>*<span class="i">$NumOfTripleBonds</span><span class="sc">;</span>
|
|
|
1017 1004
|
|
|
1018 1005 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfSigmaBonds</span><span class="cm">,</span> <span class="i">$NumOfPiBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1019 1006 <span class="s">}</span>
|
|
|
1020 1007
|
|
|
1021 1008 <span class="c"># Get information related to atoms for all heavy atoms attached to an atom..</span>
|
|
|
1022 1009 <span class="c">#</span>
|
|
|
1023 <a name="GetHeavyAtomNeighborsAtomInformation-"></a>1010 <span class="k">sub </span><span class="m">GetHeavyAtomNeighborsAtomInformation</span> <span class="s">{</span>
|
|
|
1024 1011 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1025 1012
|
|
|
1026 1013 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighborsAtomInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1027 1014 <span class="s">}</span>
|
|
|
1028 1015
|
|
|
1029 1016 <span class="c"># Get information related to atoms for all non-hydrogen atoms attached to an atom..</span>
|
|
|
1030 1017 <span class="c">#</span>
|
|
|
1031 1018 <span class="c"># The following values are returned:</span>
|
|
|
1032 1019 <span class="c"># . Number of non-hydrogen atom neighbors</span>
|
|
|
1033 1020 <span class="c"># . A reference to an array containing atom objects correpsonding to non-hydrogen</span>
|
|
|
1034 1021 <span class="c"># atom neighbors</span>
|
|
|
1035 1022 <span class="c"># . Number of different types of non-hydrogen atom neighbors</span>
|
|
|
1036 1023 <span class="c"># . A reference to a hash containing atom symbol as key with value corresponding</span>
|
|
|
1037 1024 <span class="c"># to its count for non-hydrogen atom neighbors</span>
|
|
|
1038 1025 <span class="c">#</span>
|
|
|
1039 <a name="GetNonHydrogenAtomNeighborsAtomInformation-"></a>1026 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighborsAtomInformation</span> <span class="s">{</span>
|
|
|
1040 1027 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1041 1028
|
|
|
1042 1029 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1043 1030 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1044 1031 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1045 1032 <span class="s">}</span>
|
|
|
1046 1033 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomNeighbor</span><span class="cm">,</span> <span class="i">$NumOfAtomNeighbors</span><span class="cm">,</span> <span class="i">$NumOfAtomNeighborsType</span><span class="cm">,</span> <span class="i">@AtomNeighbors</span><span class="cm">,</span> <span class="i">%AtomNeighborsTypeMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1047 1034
|
|
|
1048 1035 <span class="i">$NumOfAtomNeighbors</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">@AtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1049 1036 <span class="i">$NumOfAtomNeighborsType</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">%AtomNeighborsTypeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1050 1037
|
|
|
1051 1038 <span class="i">@AtomNeighbors</span> = <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1052 1039 <span class="i">$NumOfAtomNeighbors</span> = <span class="k">scalar</span> <span class="i">@AtomNeighbors</span><span class="sc">;</span>
|
|
|
1053 1040
|
|
|
1054 1041 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1055 1042 <span class="i">$AtomSymbol</span> = <span class="i">$AtomNeighbor</span>->{<span class="w">AtomSymbol</span>}<span class="sc">;</span>
|
|
|
1056 1043 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1057 1044 <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
1058 1045 <span class="s">}</span>
|
|
|
1059 1046 <span class="k">else</span> <span class="s">{</span>
|
|
|
1060 1047 <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1061 1048 <span class="i">$NumOfAtomNeighborsType</span>++<span class="sc">;</span>
|
|
|
1062 1049 <span class="s">}</span>
|
|
|
1063 1050 <span class="s">}</span>
|
|
|
1064 1051
|
|
|
1065 1052 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfAtomNeighbors</span><span class="cm">,</span> \<span class="i">@AtomNeighbors</span><span class="cm">,</span> <span class="i">$NumOfAtomNeighborsType</span><span class="cm">,</span> \<span class="i">%AtomNeighborsTypeMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1066 1053 <span class="s">}</span>
|
|
|
1067 1054
|
|
|
1068 1055 <span class="c"># Get information related to bonds for all heavy atoms attached to an atom..</span>
|
|
|
1069 1056 <span class="c">#</span>
|
|
|
1070 <a name="GetHeavyAtomNeighborsBondformation-"></a>1057 <span class="k">sub </span><span class="m">GetHeavyAtomNeighborsBondformation</span> <span class="s">{</span>
|
|
|
1071 1058 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1072 1059
|
|
|
1073 1060 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighborsBondInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1074 1061 <span class="s">}</span>
|
|
|
1075 1062
|
|
|
1076 1063 <span class="c"># Get information related to bonds for all non-hydrogen atoms attached to an atom..</span>
|
|
|
1077 1064 <span class="c">#</span>
|
|
|
1078 1065 <span class="c"># The following values are returned:</span>
|
|
|
1079 1066 <span class="c"># . Number of bonds to non-hydrogen atom neighbors</span>
|
|
|
1080 1067 <span class="c"># . A reference to an array containing bond objects correpsonding to non-hydrogen</span>
|
|
|
1081 1068 <span class="c"># atom neighbors</span>
|
|
|
1082 1069 <span class="c"># . A reference to a hash containing bond type as key with value corresponding</span>
|
|
|
1083 1070 <span class="c"># to its count for non-hydrogen atom neighbors. Bond types are: Single, Double or Triple</span>
|
|
|
1084 1071 <span class="c"># . A reference to a hash containing atom symbol as key pointing to bond type as second</span>
|
|
|
1085 1072 <span class="c"># key with values correponding to count of bond types for atom symbol for non-hydrogen</span>
|
|
|
1086 1073 <span class="c"># atom neighbors</span>
|
|
|
1087 1074 <span class="c"># . A reference to a hash containing atom symbol as key pointing to bond type as second</span>
|
|
|
1088 1075 <span class="c"># key with values correponding to atom objects array involved in corresponding bond type for</span>
|
|
|
1089 1076 <span class="c"># atom symbol for non-hydrogen atom neighbors</span>
|
|
|
1090 1077 <span class="c">#</span>
|
|
|
1091 <a name="GetNonHydrogenAtomNeighborsBondInformation-"></a>1078 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighborsBondInformation</span> <span class="s">{</span>
|
|
|
1092 1079 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1093 1080
|
|
|
1094 1081 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1095 1082 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1096 1083 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1097 1084 <span class="s">}</span>
|
|
|
1098 1085 <span class="k">my</span><span class="s">(</span><span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondedAtomSymbol</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$None</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="cm">,</span> <span class="i">%BondTypeCountMap</span><span class="cm">,</span> <span class="i">%AtomsBondTypesCountMap</span><span class="cm">,</span> <span class="i">%AtomsBondTypeAtomsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1099 1086
|
|
|
1100 1087 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1101 1088 <span class="i">%BondTypeCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1102 1089 <span class="i">%AtomsBondTypesCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">%AtomsBondTypeAtomsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1103 1090
|
|
|
1104 1091 <span class="i">$BondTypeCountMap</span>{<span class="w">Single</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
1105 1092 <span class="i">$BondTypeCountMap</span>{<span class="w">Double</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
1106 1093 <span class="i">$BondTypeCountMap</span>{<span class="w">Triple</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
1107 1094
|
|
|
1108 1095 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1109 1096 <span class="i">$NumOfBonds</span> = <span class="k">scalar</span> <span class="i">@Bonds</span><span class="sc">;</span>
|
|
|
1110 1097
|
|
|
1111 1098 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1112 1099 <span class="i">$BondType</span> = <span class="i">$Bond</span><span class="i">->IsSingle</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"Single"</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsDouble</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"Double"</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsTriple</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"Triple"</span> <span class="co">:</span> <span class="q">""</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1113 1100 <span class="k">if</span> <span class="s">(</span>!<span class="i">$BondType</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1114 1101 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
1115 1102 <span class="s">}</span>
|
|
|
1116 1103
|
|
|
1117 1104 <span class="c"># Track bond types...</span>
|
|
|
1118 1105 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1119 1106 <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
1120 1107 <span class="s">}</span>
|
|
|
1121 1108 <span class="k">else</span> <span class="s">{</span>
|
|
|
1122 1109 <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1123 1110 <span class="s">}</span>
|
|
|
1124 1111
|
|
|
1125 1112 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1126 1113 <span class="i">$BondedAtomSymbol</span> = <span class="i">$BondedAtom</span>->{<span class="w">AtomSymbol</span>}<span class="sc">;</span>
|
|
|
1127 1114
|
|
|
1128 1115 <span class="c"># Track bond types count for atom types involved in specific bond types...</span>
|
|
|
1129 1116 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1130 1117 <span class="i">%</span>{<span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1131 1118 <span class="s">}</span>
|
|
|
1132 1119 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1133 1120 <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
1134 1121 <span class="s">}</span>
|
|
|
1135 1122 <span class="k">else</span> <span class="s">{</span>
|
|
|
1136 1123 <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1137 1124 <span class="s">}</span>
|
|
|
1138 1125
|
|
|
1139 1126 <span class="c"># Track atoms involved in specific bond types for specific atom types...</span>
|
|
|
1140 1127 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1141 1128 <span class="i">%</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1142 1129 <span class="s">}</span>
|
|
|
1143 1130 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1144 1131 <span class="i">@</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1145 1132 <span class="s">}</span>
|
|
|
1146 1133 <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}}<span class="cm">,</span> <span class="i">$BondedAtom</span><span class="sc">;</span>
|
|
|
1147 1134 <span class="s">}</span>
|
|
|
1148 1135
|
|
|
1149 1136 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfBonds</span><span class="cm">,</span> \<span class="i">@Bonds</span><span class="cm">,</span> \<span class="i">%BondTypeCountMap</span><span class="cm">,</span> \<span class="i">%AtomsBondTypesCountMap</span><span class="cm">,</span> \<span class="i">%AtomsBondTypeAtomsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1150 1137 <span class="s">}</span>
|
|
|
1151 1138
|
|
|
1152 1139 <span class="c"># Get number of bonds to hydrogen atoms...</span>
|
|
|
1153 <a name="GetNumOfBondsToHydrogenAtoms-"></a>1140 <span class="k">sub </span><span class="m">GetNumOfBondsToHydrogenAtoms</span> <span class="s">{</span>
|
|
|
1154 1141 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1155 1142 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1156 1143
|
|
|
1157 1144 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1158 1145
|
|
|
1159 1146 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1160 1147 <span class="s">}</span>
|
|
|
1161 1148
|
|
|
1162 1149 <span class="c"># Get sum of bond orders to all bonded atoms...</span>
|
|
|
1163 1150 <span class="c">#</span>
|
|
|
1164 <a name="GetSumOfBondOrders-"></a>1151 <span class="k">sub </span><span class="m">GetSumOfBondOrders</span> <span class="s">{</span>
|
|
|
1165 1152 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1166 1153
|
|
|
1167 1154 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1168 1155 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
1169 1156 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1170 1157 <span class="s">}</span>
|
|
|
1171 1158
|
|
|
1172 1159 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1173 1160 <span class="s">}</span>
|
|
|
1174 1161
|
|
|
1175 1162 <span class="c"># Get sum of bond orders to non-hydrogen atoms only...</span>
|
|
|
1176 1163 <span class="c">#</span>
|
|
|
1177 <a name="GetSumOfBondOrdersToHeavyAtoms-"></a>1164 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToHeavyAtoms</span> <span class="s">{</span>
|
|
|
1178 1165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1179 1166
|
|
|
1180 1167 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1181 1168 <span class="s">}</span>
|
|
|
1182 1169
|
|
|
1183 1170 <span class="c"># Get sum of bond orders to non-hydrogen atoms only...</span>
|
|
|
1184 1171 <span class="c">#</span>
|
|
|
1185 <a name="GetSumOfBondOrdersToNonHydrogenAtoms-"></a>1172 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
1186 1173 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1187 1174
|
|
|
1188 1175 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1189 1176 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1190 1177 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1191 1178 <span class="s">}</span>
|
|
|
1192 1179 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1193 1180
|
|
|
1194 1181 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetSumOfBondOrders</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1195 1182 <span class="s">}</span>
|
|
|
1196 1183
|
|
|
1197 1184 <span class="c"># Get sum of bond orders to hydrogen atoms only...</span>
|
|
|
1198 1185 <span class="c">#</span>
|
|
|
1199 <a name="GetSumOfBondOrdersToHydrogenAtoms-"></a>1186 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToHydrogenAtoms</span> <span class="s">{</span>
|
|
|
1200 1187 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1201 1188
|
|
|
1202 1189 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1203 1190 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
1204 1191 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1205 1192 <span class="s">}</span>
|
|
|
1206 1193 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1207 1194
|
|
|
1208 1195 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetSumOfBondOrders</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1209 1196 <span class="s">}</span>
|
|
|
1210 1197
|
|
|
1211 1198 <span class="c"># Get sum of bond orders to all bonded atoms, non-hydrogen or hydrogen bonded atoms...</span>
|
|
|
1212 1199 <span class="c">#</span>
|
|
|
1213 <a name="_GetSumOfBondOrders-"></a>1200 <span class="k">sub </span><span class="m">_GetSumOfBondOrders</span> <span class="s">{</span>
|
|
|
1214 1201 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1215 1202
|
|
|
1216 1203 <span class="c"># Check flags...</span>
|
|
|
1217 1204 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1218 1205 <span class="i">$ToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1219 1206 <span class="s">}</span>
|
|
|
1220 1207 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1221 1208 <span class="i">$ToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1222 1209 <span class="s">}</span>
|
|
|
1223 1210 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1224 1211 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1225 1212
|
|
|
1226 1213 <span class="k">if</span> <span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1227 1214 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1228 1215 <span class="s">}</span>
|
|
|
1229 1216 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1230 1217 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1231 1218 <span class="s">}</span>
|
|
|
1232 1219 <span class="k">else</span> <span class="s">{</span>
|
|
|
1233 1220 <span class="c"># All bonds...</span>
|
|
|
1234 1221 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1235 1222 <span class="s">}</span>
|
|
|
1236 1223
|
|
|
1237 1224 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1238 1225 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1239 1226 <span class="i">$SumOfBondOrders</span> += <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1240 1227 <span class="s">}</span>
|
|
|
1241 1228
|
|
|
1242 1229 <span class="k">if</span> <span class="s">(</span><span class="i">$SumOfBondOrders</span> =~ <span class="q">/\./</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1243 1230 <span class="c">#</span>
|
|
|
1244 1231 <span class="c"># Change any fractional bond order to next largest integer...</span>
|
|
|
1245 1232 <span class="c">#</span>
|
|
|
1246 1233 <span class="c"># As long as aromatic bond orders in a ring are correctly using using 4n + 2 Huckel rule</span>
|
|
|
1247 1234 <span class="c"># (BondOrder: 1.5) or explicity set as Kekule bonds (alternate single/double),</span>
|
|
|
1248 1235 <span class="c"># SumOfBondOrders should add up to an integer.</span>
|
|
|
1249 1236 <span class="c">#</span>
|
|
|
1250 1237 <span class="i">$SumOfBondOrders</span> = <span class="i">ceil</span><span class="s">(</span><span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1251 1238 <span class="s">}</span>
|
|
|
1252 1239
|
|
|
1253 1240 <span class="k">return</span> <span class="i">$SumOfBondOrders</span><span class="sc">;</span>
|
|
|
1254 1241 <span class="s">}</span>
|
|
|
1255 1242
|
|
|
1256 1243 <span class="c"># Get largest bond order to any bonded atoms...</span>
|
|
|
1257 1244 <span class="c">#</span>
|
|
|
1258 <a name="GetLargestBondOrder-"></a>1245 <span class="k">sub </span><span class="m">GetLargestBondOrder</span> <span class="s">{</span>
|
|
|
1259 1246 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1260 1247
|
|
|
1261 1248 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1262 1249 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1263 1250 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1264 1251 <span class="s">}</span>
|
|
|
1265 1252
|
|
|
1266 1253 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetLargestBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1267 1254 <span class="s">}</span>
|
|
|
1268 1255
|
|
|
1269 1256 <span class="c"># Get largest bond order to bonded non-hydrogen atoms...</span>
|
|
|
1270 1257 <span class="c">#</span>
|
|
|
1271 <a name="GetLargestBondOrderToHeavyAtoms-"></a>1258 <span class="k">sub </span><span class="m">GetLargestBondOrderToHeavyAtoms</span> <span class="s">{</span>
|
|
|
1272 1259 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1273 1260
|
|
|
1274 1261 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1275 1262 <span class="s">}</span>
|
|
|
1276 1263
|
|
|
1277 1264 <span class="c"># Get largest bond order to bonded non-hydrogen atoms...</span>
|
|
|
1278 1265 <span class="c">#</span>
|
|
|
1279 <a name="GetLargestBondOrderToNonHydrogenAtoms-"></a>1266 <span class="k">sub </span><span class="m">GetLargestBondOrderToNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
1280 1267 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1281 1268
|
|
|
1282 1269 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1283 1270 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
1284 1271 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1285 1272 <span class="s">}</span>
|
|
|
1286 1273
|
|
|
1287 1274 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1288 1275
|
|
|
1289 1276 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetLargestBondOrder</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1290 1277 <span class="s">}</span>
|
|
|
1291 1278
|
|
|
1292 1279 <span class="c"># Get largest bond order to all bonded atoms, non-hydrogen or hydrogen bonded atoms...</span>
|
|
|
1293 1280 <span class="c">#</span>
|
|
|
1294 <a name="_GetLargestBondOrder-"></a>1281 <span class="k">sub </span><span class="m">_GetLargestBondOrder</span> <span class="s">{</span>
|
|
|
1295 1282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1296 1283
|
|
|
1297 1284 <span class="c"># Check flags...</span>
|
|
|
1298 1285 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1299 1286 <span class="i">$ToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1300 1287 <span class="s">}</span>
|
|
|
1301 1288 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1302 1289 <span class="i">$ToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1303 1290 <span class="s">}</span>
|
|
|
1304 1291 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$LargestBondOrder</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1305 1292 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1306 1293
|
|
|
1307 1294 <span class="k">if</span> <span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1308 1295 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1309 1296 <span class="s">}</span>
|
|
|
1310 1297 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1311 1298 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1312 1299 <span class="s">}</span>
|
|
|
1313 1300 <span class="k">else</span> <span class="s">{</span>
|
|
|
1314 1301 <span class="c"># All bonds...</span>
|
|
|
1315 1302 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1316 1303 <span class="s">}</span>
|
|
|
1317 1304
|
|
|
1318 1305 <span class="i">$LargestBondOrder</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1319 1306 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1320 1307 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1321 1308 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> > <span class="i">$LargestBondOrder</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1322 1309 <span class="i">$LargestBondOrder</span> = <span class="i">$BondOrder</span><span class="sc">;</span>
|
|
|
1323 1310 <span class="s">}</span>
|
|
|
1324 1311 <span class="s">}</span>
|
|
|
1325 1312
|
|
|
1326 1313 <span class="k">return</span> <span class="i">$LargestBondOrder</span><span class="sc">;</span>
|
|
|
1327 1314 <span class="s">}</span>
|
|
|
1328 1315
|
|
|
1329 1316 <span class="c"># Get number of implicit hydrogen for atom...</span>
|
|
|
1330 1317 <span class="c">#</span>
|
|
|
1331 <a name="GetImplicitHydrogens-"></a>1318 <span class="k">sub </span><span class="m">GetImplicitHydrogens</span> <span class="s">{</span>
|
|
|
1332 1319 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1333 1320
|
|
|
1334 1321 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1335 1322 <span class="s">}</span>
|
|
|
1336 1323
|
|
|
1337 1324 <span class="c"># Get number of implicit hydrogen for atom...</span>
|
|
|
1338 1325 <span class="c">#</span>
|
|
|
1339 <a name="GetNumOfImplicitHydrogens-"></a>1326 <span class="k">sub </span><span class="m">GetNumOfImplicitHydrogens</span> <span class="s">{</span>
|
|
|
1340 1327 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1341 1328
|
|
|
1342 1329 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1343 1330 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1344 1331 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1345 1332 <span class="s">}</span>
|
|
|
1346 1333
|
|
|
1347 1334 <span class="c"># Is ImplicitHydrogens property explicitly set?</span>
|
|
|
1348 1335 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1349 1336 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1350 1337 <span class="s">}</span>
|
|
|
1351 1338
|
|
|
1352 1339 <span class="c"># Is it an element symbol?</span>
|
|
|
1353 1340 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1354 1341 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1355 1342 <span class="s">}</span>
|
|
|
1356 1343
|
|
|
1357 1344 <span class="k">my</span><span class="s">(</span><span class="i">$ImplicitHydrogens</span><span class="cm">,</span> <span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1358 1345
|
|
|
1359 1346 <span class="i">$ImplicitHydrogens</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1360 1347 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1361 1348 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->GetPotentialTotalCommonValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1362 1349
|
|
|
1363 1350 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1364 1351 <span class="c"># Subtract sum of bond orders to non-hydrogen and hydrogen atom neighbors...</span>
|
|
|
1365 1352 <span class="i">$ImplicitHydrogens</span> = <span class="i">$PotentialTotalValence</span> - <span class="i">$SumOfBondOrders</span><span class="sc">;</span>
|
|
|
1366 1353 <span class="s">}</span>
|
|
|
1367 1354
|
|
|
1368 1355 <span class="k">return</span> <span class="i">$ImplicitHydrogens</span> > <span class="n">0</span> ? <span class="i">$ImplicitHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1369 1356 <span class="s">}</span>
|
|
|
1370 1357
|
|
|
1371 1358 <span class="c"># Get number of bonds available to form additional bonds with heavy atoms, excluding</span>
|
|
|
1372 1359 <span class="c"># any implicit bonds to hydrogens set using ImplicitHydrogens property.</span>
|
|
|
1373 1360 <span class="c">#</span>
|
|
|
1374 1361 <span class="c"># It's different from number of implicit or missing hydrogens, both of which are equivalent.</span>
|
|
|
1375 1362 <span class="c">#</span>
|
|
|
1376 1363 <span class="c"># For example, in a SMILES string, [nH] ring atom corresponds to an aromatic nitrogen.</span>
|
|
|
1377 1364 <span class="c"># Although the hydrogen specified for n is treated internally as implicit hydrogen and shows</span>
|
|
|
1378 1365 <span class="c"># up in missing hydrogen count, it's not available to participate in double bonds to additional</span>
|
|
|
1379 1366 <span class="c"># heavy atoms.</span>
|
|
|
1380 1367 <span class="c">#</span>
|
|
|
1381 <a name="GetNumOfBondsAvailableForHeavyAtoms-"></a>1368 <span class="k">sub </span><span class="m">GetNumOfBondsAvailableForHeavyAtoms</span> <span class="s">{</span>
|
|
|
1382 1369 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1383 1370
|
|
|
1384 1371 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfBondsAvailableForNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1385 1372 <span class="s">}</span>
|
|
|
1386 1373
|
|
|
1387 1374 <span class="c"># It's another name for GetNumOfBondsAvailableForHeavyAtoms</span>
|
|
|
1388 1375 <span class="c">#</span>
|
|
|
1389 <a name="GetNumOfBondsAvailableForNonHydrogenAtoms-"></a>1376 <span class="k">sub </span><span class="m">GetNumOfBondsAvailableForNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
1390 1377 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1391 1378 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfAvailableBonds</span><span class="cm">,</span> <span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1392 1379
|
|
|
1393 1380 <span class="i">$NumOfAvailableBonds</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1394 1381
|
|
|
1395 1382 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1396 1383 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->GetPotentialTotalCommonValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1397 1384
|
|
|
1398 1385 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1399 1386 <span class="c"># Subtract sum of bond orders to non-hydrogen and hydrogen atom neighbors...</span>
|
|
|
1400 1387 <span class="i">$NumOfAvailableBonds</span> = <span class="i">$PotentialTotalValence</span> - <span class="i">$SumOfBondOrders</span><span class="sc">;</span>
|
|
|
1401 1388 <span class="s">}</span>
|
|
|
1402 1389
|
|
|
1403 1390 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1404 1391 <span class="i">$NumOfAvailableBonds</span> -= <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1405 1392 <span class="s">}</span>
|
|
|
1406 1393
|
|
|
1407 1394 <span class="k">return</span> <span class="i">$NumOfAvailableBonds</span> > <span class="n">0</span> ? <span class="i">$NumOfAvailableBonds</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1408 1395 <span class="s">}</span>
|
|
|
1409 1396
|
|
|
1410 1397 <span class="c"># Disable setting of explicit hydrogens property...</span>
|
|
|
1411 <a name="SetExplicitHydrogens-"></a>1398 <span class="k">sub </span><span class="m">SetExplicitHydrogens</span> <span class="s">{</span>
|
|
|
1412 1399 <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>
|
|
|
1413 1400
|
|
|
1414 1401 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetExplicitHydrogens: Setting of explicit hydrogens is not supported..."</span><span class="sc">;</span>
|
|
|
1415 1402
|
|
|
1416 1403 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1417 1404 <span class="s">}</span>
|
|
|
1418 1405
|
|
|
1419 1406 <span class="c"># Get number of explicit hydrogens for atom...</span>
|
|
|
1420 1407 <span class="c">#</span>
|
|
|
1421 <a name="GetExplicitHydrogens-"></a>1408 <span class="k">sub </span><span class="m">GetExplicitHydrogens</span> <span class="s">{</span>
|
|
|
1422 1409 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1423 1410
|
|
|
1424 1411 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1425 1412 <span class="s">}</span>
|
|
|
1426 1413
|
|
|
1427 1414 <span class="c"># Get number of explicit hydrogens for atom...</span>
|
|
|
1428 1415 <span class="c">#</span>
|
|
|
1429 <a name="GetNumOfExplicitHydrogens-"></a>1416 <span class="k">sub </span><span class="m">GetNumOfExplicitHydrogens</span> <span class="s">{</span>
|
|
|
1430 1417 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1431 1418 <span class="k">my</span><span class="s">(</span><span class="i">$HydrogenAtomNbrs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1432 1419
|
|
|
1433 1420 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1434 1421 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1435 1422 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1436 1423 <span class="s">}</span>
|
|
|
1437 1424
|
|
|
1438 1425 <span class="i">$HydrogenAtomNbrs</span> = <span class="i">$This</span><span class="i">->GetNumOfHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1439 1426
|
|
|
1440 1427 <span class="k">return</span> <span class="k">defined</span> <span class="i">$HydrogenAtomNbrs</span> ? <span class="i">$HydrogenAtomNbrs</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1441 1428 <span class="s">}</span>
|
|
|
1442 1429
|
|
|
1443 1430 <span class="c"># Get num of missing hydrogens...</span>
|
|
|
1444 1431 <span class="c">#</span>
|
|
|
1445 <a name="GetMissingHydrogens-"></a>1432 <span class="k">sub </span><span class="m">GetMissingHydrogens</span> <span class="s">{</span>
|
|
|
1446 1433 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1447 1434
|
|
|
1448 1435 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1449 1436 <span class="s">}</span>
|
|
|
1450 1437
|
|
|
1451 1438 <span class="c"># Get num of missing hydrogens...</span>
|
|
|
1452 1439 <span class="c">#</span>
|
|
|
1453 <a name="GetNumOfMissingHydrogens-"></a>1440 <span class="k">sub </span><span class="m">GetNumOfMissingHydrogens</span> <span class="s">{</span>
|
|
|
1454 1441 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1455 1442
|
|
|
1456 1443 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1457 1444 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1458 1445 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1459 1446 <span class="s">}</span>
|
|
|
1460 1447
|
|
|
1461 1448 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1462 1449 <span class="s">}</span>
|
|
|
1463 1450
|
|
|
1464 1451 <span class="c"># Get total number of hydrogens...</span>
|
|
|
1465 1452 <span class="c">#</span>
|
|
|
1466 <a name="GetHydrogens-"></a>1453 <span class="k">sub </span><span class="m">GetHydrogens</span> <span class="s">{</span>
|
|
|
1467 1454 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1468 1455
|
|
|
1469 1456 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1470 1457 <span class="s">}</span>
|
|
|
1471 1458
|
|
|
1472 1459 <span class="c"># Get total number of hydrogens...</span>
|
|
|
1473 1460 <span class="c">#</span>
|
|
|
1474 <a name="GetNumOfHydrogens-"></a>1461 <span class="k">sub </span><span class="m">GetNumOfHydrogens</span> <span class="s">{</span>
|
|
|
1475 1462 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1476 1463
|
|
|
1477 1464 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1478 1465 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
1479 1466 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1480 1467 <span class="s">}</span>
|
|
|
1481 1468
|
|
|
1482 1469 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1483 1470 <span class="s">}</span>
|
|
|
1484 1471
|
|
|
1485 1472 <span class="c"># Valence corresponds to the number of electrons used by an atom in bonding:</span>
|
|
|
1486 1473 <span class="c">#</span>
|
|
|
1487 1474 <span class="c"># Valence = ValenceElectrons - ValenceFreeElectrons = BondingElectrons</span>
|
|
|
1488 1475 <span class="c">#</span>
|
|
|
1489 1476 <span class="c"># Single, double, triple bonds with bond orders of 1, 2 and 3 correspond to contribution of</span>
|
|
|
1490 1477 <span class="c"># 1, 2, and 3 bonding electrons. So Valence can be computed using:</span>
|
|
|
1491 1478 <span class="c">#</span>
|
|
|
1492 1479 <span class="c"># Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge</span>
|
|
|
1493 1480 <span class="c">#</span>
|
|
|
1494 1481 <span class="c"># where positive and negative values of FormalCharge increase and decrease the number</span>
|
|
|
1495 1482 <span class="c"># of bonding electrons respectively.</span>
|
|
|
1496 1483 <span class="c">#</span>
|
|
|
1497 1484 <span class="c"># The current release of MayaChemTools supports the following three valence models, which</span>
|
|
|
1498 1485 <span class="c"># are used during calculation of implicit hydrogens: MDLValenceModel, DaylightValenceModel,</span>
|
|
|
1499 1486 <span class="c"># InternalValenceModel or MayaChemToolsValenceModel.</span>
|
|
|
1500 1487 <span class="c">#</span>
|
|
|
1501 1488 <span class="c"># Notes:</span>
|
|
|
1502 1489 <span class="c"># . This doesn't always corresponds to explicit valence.</span>
|
|
|
1503 1490 <span class="c"># . Missing hydrogens are included in the valence.</span>
|
|
|
1504 1491 <span class="c"># . For neutral molecules, valence and sum of bond order are equal.</span>
|
|
|
1505 1492 <span class="c"># . For molecules containing only single bonds, SumOfBondOrders and NumOfBonds are equal.</span>
|
|
|
1506 1493 <span class="c"># . Free radical electrons lead to the decrease in valence. For atoms with explicit assignment</span>
|
|
|
1507 1494 <span class="c"># of SpinMultiplicity property values corresponding to Singlet (two unparied electrons</span>
|
|
|
1508 1495 <span class="c"># corresponding to one spin state), Doublet (free radical; an unpaired electron corresponding</span>
|
|
|
1509 1496 <span class="c"># to two spin states), and Triplet (two unparied electrons corresponding to three spin states;</span>
|
|
|
1510 1497 <span class="c"># divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:</span>
|
|
|
1511 1498 <span class="c">#</span>
|
|
|
1512 1499 <span class="c"># SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1 (one valence electron not available for bonding)</span>
|
|
|
1513 1500 <span class="c"># SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2 (two valence electrons not available for bonding)</span>
|
|
|
1514 1501 <span class="c">#</span>
|
|
|
1515 <a name="GetValence-"></a>1502 <span class="k">sub </span><span class="m">GetValence</span> <span class="s">{</span>
|
|
|
1516 1503 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1517 1504
|
|
|
1518 1505 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1519 1506 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
1520 1507 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1521 1508 <span class="s">}</span>
|
|
|
1522 1509
|
|
|
1523 1510 <span class="c"># Is Valence property explicitly set?</span>
|
|
|
1524 1511 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Valence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1525 1512 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Valence'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1526 1513 <span class="s">}</span>
|
|
|
1527 1514 <span class="k">my</span><span class="s">(</span><span class="i">$Valence</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1528 1515
|
|
|
1529 1516 <span class="i">$Valence</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1530 1517
|
|
|
1531 1518 <span class="k">return</span> <span class="i">$Valence</span> > <span class="n">0</span> ? <span class="i">$Valence</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1532 1519 <span class="s">}</span>
|
|
|
1533 1520
|
|
|
1534 1521 <span class="c"># Get free non-bodning valence electrons left on atom after taking into account</span>
|
|
|
1535 1522 <span class="c"># sum of bond orders, missing hydrogens and formal charged on the atom. Free</span>
|
|
|
1536 1523 <span class="c"># radical electrons are included in the valence free electrons count by default.</span>
|
|
|
1537 1524 <span class="c">#</span>
|
|
|
1538 1525 <span class="c"># Valence corresponds to number of electrons used by atom in bonding:</span>
|
|
|
1539 1526 <span class="c">#</span>
|
|
|
1540 1527 <span class="c"># Valence = ValenceElectrons - ValenceFreeElectrons</span>
|
|
|
1541 1528 <span class="c">#</span>
|
|
|
1542 1529 <span class="c"># Additionally, valence can also be calculated by:</span>
|
|
|
1543 1530 <span class="c">#</span>
|
|
|
1544 1531 <span class="c"># Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge</span>
|
|
|
1545 1532 <span class="c">#</span>
|
|
|
1546 1533 <span class="c"># Valence and SumOfBondOrders are equal for neutral molecules.</span>
|
|
|
1547 1534 <span class="c">#</span>
|
|
|
1548 1535 <span class="c"># From two formulas for Valence described above, non-bonding free electrons</span>
|
|
|
1549 1536 <span class="c"># left can be computed by:</span>
|
|
|
1550 1537 <span class="c">#</span>
|
|
|
1551 1538 <span class="c"># ValenceFreeElectrons = ValenceElectrons - Valence</span>
|
|
|
1552 1539 <span class="c"># = ValenceElectrons - SumOfBondOrders -</span>
|
|
|
1553 1540 <span class="c"># NumOfMissingHydrogens - FormalCharge</span>
|
|
|
1554 1541 <span class="c">#</span>
|
|
|
1555 1542 <span class="c"># . Notes:</span>
|
|
|
1556 1543 <span class="c"># . Missing hydrogens are excluded from the valence free electrons.</span>
|
|
|
1557 1544 <span class="c"># . Any free radical electrons are considered part of the valence free electrons</span>
|
|
|
1558 1545 <span class="c"># by default.</span>
|
|
|
1559 1546 <span class="c">#</span>
|
|
|
1560 1547 <span class="c"># Examples:</span>
|
|
|
1561 1548 <span class="c">#</span>
|
|
|
1562 1549 <span class="c"># o NH3: ValenceFreeElectrons = 5 - 3 = 5 - 3 - 0 - 0 = 2</span>
|
|
|
1563 1550 <span class="c"># o NH2: ValenceFreeElectrons = 5 - 3 = 5 - 2 - 1 - 0 = 2</span>
|
|
|
1564 1551 <span class="c"># o NH4+; ValenceFreeElectrons = 5 - 5 = 5 - 4 - 0 - 1 = 0</span>
|
|
|
1565 1552 <span class="c"># o NH3+; ValenceFreeElectrons = 5 - 5 = 5 - 3 - 1 - 1 = 0</span>
|
|
|
1566 1553 <span class="c"># o C(=O)O- : ValenceFreeElectrons on O- = 6 - 0 = 6 - 1 - 0 - (-1) = 6</span>
|
|
|
1567 1554 <span class="c"># o C(=O)O- : ValenceFreeElectrons on =O = 6 - 2 = 6 - 2 - 0 - 0 = 4</span>
|
|
|
1568 1555 <span class="c">#</span>
|
|
|
1569 1556 <span class="c">#</span>
|
|
|
1570 <a name="GetValenceFreeElectrons-"></a>1557 <span class="k">sub </span><span class="m">GetValenceFreeElectrons</span> <span class="s">{</span>
|
|
|
1571 1558 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1572 1559
|
|
|
1573 1560 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1574 1561 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
1575 1562 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1576 1563 <span class="s">}</span>
|
|
|
1577 1564
|
|
|
1578 1565 <span class="c"># Is ValenceFreeElectrons property explicitly set?</span>
|
|
|
1579 1566 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceFreeElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1580 1567 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceFreeElectrons'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1581 1568 <span class="s">}</span>
|
|
|
1582 1569
|
|
|
1583 1570 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1584 1571 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1585 1572 <span class="s">}</span>
|
|
|
1586 1573
|
|
|
1587 1574 <span class="k">my</span><span class="s">(</span><span class="i">$ValenceFreeElectrons</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1588 1575
|
|
|
1589 1576 <span class="i">$ValenceFreeElectrons</span> = <span class="i">$This</span><span class="i">->GetValenceElectrons</span><span class="s">(</span><span class="s">)</span> - <span class="i">$This</span><span class="i">->GetValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1590 1577 <span class="k">if</span> <span class="s">(</span><span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1591 1578 <span class="i">$ValenceFreeElectrons</span> -= <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1592 1579 <span class="s">}</span>
|
|
|
1593 1580
|
|
|
1594 1581 <span class="k">return</span> <span class="i">$ValenceFreeElectrons</span> > <span class="n">0</span> ? <span class="i">$ValenceFreeElectrons</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1595 1582 <span class="s">}</span>
|
|
|
1596 1583
|
|
|
1597 1584 <span class="c"># Get potential total common valence for calculating the number of implicit hydrogens</span>
|
|
|
1598 1585 <span class="c"># using the specified common valence model or default internal model for a molecule...</span>
|
|
|
1599 1586 <span class="c">#</span>
|
|
|
1600 <a name="GetPotentialTotalCommonValence-"></a>1587 <span class="k">sub </span><span class="m">GetPotentialTotalCommonValence</span> <span class="s">{</span>
|
|
|
1601 1588 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1602 1589
|
|
|
1603 1590 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1604 1591 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
1605 1592 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1606 1593 <span class="s">}</span>
|
|
|
1607 1594 <span class="k">my</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$ValenceModel</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1608 1595
|
|
|
1609 1596 <span class="i">$PotentialTotalValence</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1610 1597 <span class="i">$ValenceModel</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="i">->GetValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1611 1598
|
|
|
1612 1599 <span class="j">VALENCEMODEL:</span> <span class="s">{</span>
|
|
|
1613 1600 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> =~ <span class="q">/^MDLValenceModel$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1614 1601 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingMDLValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1615 1602 <span class="k">last</span> <span class="j">VALENCEMODEL</span><span class="sc">;</span>
|
|
|
1616 1603 <span class="s">}</span>
|
|
|
1617 1604 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> =~ <span class="q">/^DaylightValenceModel$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1618 1605 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingDaylightValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1619 1606 <span class="k">last</span> <span class="j">VALENCEMODEL</span><span class="sc">;</span>
|
|
|
1620 1607 <span class="s">}</span>
|
|
|
1621 1608 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> !~ <span class="q">/^(InternalValenceModel|MayaChemToolsValenceModel)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1622 1609 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetPotentialTotalCommonValence: The current release of MayaChemTools doesn't support the specified valence model $ValenceModel. Supported valence models: MDLValenceModel, DaylightValenceModel, InternalValenceModel. Using internal valence model..."</span><span class="sc">;</span>
|
|
|
1623 1610 <span class="s">}</span>
|
|
|
1624 1611 <span class="c"># Use internal valence model as the default valence model...</span>
|
|
|
1625 1612 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingInternalValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1626 1613 <span class="s">}</span>
|
|
|
1627 1614
|
|
|
1628 1615 <span class="k">return</span> <span class="i">$PotentialTotalValence</span><span class="sc">;</span>
|
|
|
1629 1616 <span class="s">}</span>
|
|
|
1630 1617
|
|
|
1631 1618 <span class="c"># Get potential total common valence using data for MDL valence model available in file,</span>
|
|
|
1632 1619 <span class="c"># lib/data/MDLValenceModelData.csv, distributed with the package...</span>
|
|
|
1633 1620 <span class="c">#</span>
|
|
|
1634 <a name="_GetPotentialTotalCommonValenceUsingMDLValenceModel-"></a>1621 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingMDLValenceModel</span> <span class="s">{</span>
|
|
|
1635 1622 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1636 1623
|
|
|
1637 1624 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingValenceModelData</span><span class="s">(</span>\<span class="i">%MDLValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1638 1625
|
|
|
1639 1626 <span class="s">}</span>
|
|
|
1640 1627
|
|
|
1641 1628 <span class="c"># Get potential total common valence using data for Daylight valence model available in file,</span>
|
|
|
1642 1629 <span class="c"># lib/data/DaylightValenceModelData.csv, distributed with the release...</span>
|
|
|
1643 1630 <span class="c">#</span>
|
|
|
1644 <a name="_GetPotentialTotalCommonValenceUsingDaylightValenceModel-"></a>1631 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingDaylightValenceModel</span> <span class="s">{</span>
|
|
|
1645 1632 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1646 1633
|
|
|
1647 1634 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingValenceModelData</span><span class="s">(</span>\<span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1648 1635 <span class="s">}</span>
|
|
|
1649 1636
|
|
|
1650 1637 <span class="c"># Get potential total common valence using data for a specific valence model...</span>
|
|
|
1651 1638 <span class="c">#</span>
|
|
|
1652 <a name="_GetPotentialTotalCommonValenceUsingValenceModelData-"></a>1639 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingValenceModelData</span> <span class="s">{</span>
|
|
|
1653 1640 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ValenceModelDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1654 1641 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1655 1642
|
|
|
1656 1643 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
1657 1644 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1658 1645 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1659 1646 <span class="s">}</span>
|
|
|
1660 1647
|
|
|
1661 1648 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1662 1649
|
|
|
1663 1650 <span class="c"># Is any valence model data available for atomic number and formal charge?</span>
|
|
|
1664 1651 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ValenceModelDataRef</span>->{<span class="i">$AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1665 1652 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1666 1653 <span class="s">}</span>
|
|
|
1667 1654 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ValenceModelDataRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1668 1655 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1669 1656 <span class="s">}</span>
|
|
|
1670 1657
|
|
|
1671 1658 <span class="k">my</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="cm">,</span> <span class="i">$CurrentEffectiveValence</span><span class="cm">,</span> <span class="i">$AvailableCommonValence</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1672 1659
|
|
|
1673 1660 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1674 1661 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1675 1662 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1676 1663 <span class="s">}</span>
|
|
|
1677 1664 <span class="i">$CurrentEffectiveValence</span> = <span class="i">$SumOfBondOrders</span> + <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1678 1665
|
|
|
1679 1666 <span class="i">$PotentialTotalValence</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1680 1667 <span class="j">VALENCE:</span> <span class="k">for</span> <span class="i">$AvailableCommonValence</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ValenceModelDataRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">CommonValences</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1681 1668 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentEffectiveValence</span> <= <span class="i">$AvailableCommonValence</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1682 1669 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValence</span><span class="sc">;</span>
|
|
|
1683 1670 <span class="k">last</span> <span class="j">VALENCE</span><span class="sc">;</span>
|
|
|
1684 1671 <span class="s">}</span>
|
|
|
1685 1672 <span class="s">}</span>
|
|
|
1686 1673
|
|
|
1687 1674 <span class="k">return</span> <span class="i">$PotentialTotalValence</span><span class="sc">;</span>
|
|
|
1688 1675 <span class="s">}</span>
|
|
|
1689 1676
|
|
|
1690 1677 <span class="c">#</span>
|
|
|
1691 1678 <span class="c"># For elements with one one common valence, potential total common valence used</span>
|
|
|
1692 1679 <span class="c"># during the calculation for number of implicit hydrogens during InternalValenceMode</span>
|
|
|
1693 1680 <span class="c"># corresponds to:</span>
|
|
|
1694 1681 <span class="c">#</span>
|
|
|
1695 1682 <span class="c"># CommonValence + FormalCharge - FreeRadicalElectrons</span>
|
|
|
1696 1683 <span class="c">#</span>
|
|
|
1697 1684 <span class="c"># For elements with multiple common valences, each common valence is used to</span>
|
|
|
1698 1685 <span class="c"># calculate total potential common valence as shown above, and the first total potential</span>
|
|
|
1699 1686 <span class="c"># common valence gerater than the sum of bond orderes is selected as the final total</span>
|
|
|
1700 1687 <span class="c"># common valence.</span>
|
|
|
1701 1688 <span class="c">#</span>
|
|
|
1702 1689 <span class="c"># Group numbers > 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He)</span>
|
|
|
1703 1690 <span class="c">#</span>
|
|
|
1704 1691 <span class="c"># Formal charge sign is not adjusted. Positive and negative values result in the</span>
|
|
|
1705 1692 <span class="c"># increase and decrease of valence.</span>
|
|
|
1706 1693 <span class="c">#</span>
|
|
|
1707 1694 <span class="c"># Group 14 containing C, Si, Ge, Sn, Pb...</span>
|
|
|
1708 1695 <span class="c">#</span>
|
|
|
1709 1696 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
|
|
|
1710 1697 <span class="c"># values result in the decrease of valence.</span>
|
|
|
1711 1698 <span class="c">#</span>
|
|
|
1712 1699 <span class="c"># Group 13 containing B, Al, Ga, In, Tl...</span>
|
|
|
1713 1700 <span class="c">#</span>
|
|
|
1714 1701 <span class="c"># Formal charge sign is always reversed. Positive and negative values result in the</span>
|
|
|
1715 1702 <span class="c"># decrease and increase of valence.</span>
|
|
|
1716 1703 <span class="c">#</span>
|
|
|
1717 1704 <span class="c"># Groups 1 (H) through 12 (Zn)...</span>
|
|
|
1718 1705 <span class="c">#</span>
|
|
|
1719 1706 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
|
|
|
1720 1707 <span class="c"># values result in the decrease of valence.</span>
|
|
|
1721 1708 <span class="c">#</span>
|
|
|
1722 1709 <span class="c"># Lanthanides and actinides...</span>
|
|
|
1723 1710 <span class="c">#</span>
|
|
|
1724 1711 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
|
|
|
1725 1712 <span class="c"># values result in the decrease of valence.</span>
|
|
|
1726 1713 <span class="c">#</span>
|
|
|
1727 1714 <span class="c"># Notes:</span>
|
|
|
1728 1715 <span class="c"># . CommonValence and HighestCommonValence available from PeriodicTable module</span>
|
|
|
1729 1716 <span class="c"># are equivalent to most common and highest sum of bond orders for an element. For</span>
|
|
|
1730 1717 <span class="c"># neutral atoms involved only in single bonds, it corresponds to highest number of</span>
|
|
|
1731 1718 <span class="c"># allowed bonds for the atom.</span>
|
|
|
1732 1719 <span class="c"># . FormalCharge sign is reversed for electropositive elements with positive formal charge</span>
|
|
|
1733 1720 <span class="c"># during common valence calculations. Electropositive elements, metals and transition elements,</span>
|
|
|
1734 1721 <span class="c"># have usually plus formal charge and it leads to decrease in common valence; the negative</span>
|
|
|
1735 1722 <span class="c"># formal charge should result in the decrease of common valence.</span>
|
|
|
1736 1723 <span class="c"># . For carbon, both plus/minus formal charge cause decrease in common valence</span>
|
|
|
1737 1724 <span class="c"># . For elements on the right of carbon in periodic table, electronegative elements, plus formal</span>
|
|
|
1738 1725 <span class="c"># charge causes common valence to increase and minus formal charge cause it to decrease.</span>
|
|
|
1739 1726 <span class="c">#</span>
|
|
|
1740 <a name="_GetPotentialTotalCommonValenceUsingInternalValenceModel-"></a>1727 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingInternalValenceModel</span> <span class="s">{</span>
|
|
|
1741 1728 <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>
|
|
|
1742 1729 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1743 1730
|
|
|
1744 1731 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
1745 1732 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1746 1733 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1747 1734 <span class="s">}</span>
|
|
|
1748 1735
|
|
|
1749 1736 <span class="i">$CommonValences</span> = <span class="i">PeriodicTable::GetElementCommonValences</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1750 1737 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CommonValences</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1751 1738 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1752 1739 <span class="s">}</span>
|
|
|
1753 1740
|
|
|
1754 1741 <span class="k">my</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$AdjustedFormalCharge</span><span class="cm">,</span> <span class="i">$FreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="cm">,</span> <span class="i">$AvailableCommonValence</span><span class="cm">,</span> <span class="i">@AvailableCommonValences</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1755 1742
|
|
|
1756 1743 <span class="i">$AdjustedFormalCharge</span> = <span class="i">$This</span><span class="i">->_GetFormalChargeAdjustedForInternalValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1757 1744 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1758 1745
|
|
|
1759 1746 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1760 1747 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1761 1748 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1762 1749 <span class="s">}</span>
|
|
|
1763 1750
|
|
|
1764 1751 <span class="i">@AvailableCommonValences</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="sc">;</span>
|
|
|
1765 1752
|
|
|
1766 1753 <span class="k">if</span> <span class="s">(</span><span class="i">@AvailableCommonValences</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1767 1754 <span class="c"># Calculate potential total valence using the only available common valence...</span>
|
|
|
1768 1755 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValences</span>[<span class="n">0</span>] + <span class="i">$AdjustedFormalCharge</span> - <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span>
|
|
|
1769 1756 <span class="s">}</span>
|
|
|
1770 1757 <span class="k">else</span> <span class="s">{</span>
|
|
|
1771 1758 <span class="c"># Calculate potential total valence using common valence from a list of available valences</span>
|
|
|
1772 1759 <span class="c"># that makes it higher than sum of bond orders or using the highest common valence...</span>
|
|
|
1773 1760 <span class="j">VALENCE:</span> <span class="k">for</span> <span class="i">$AvailableCommonValence</span> <span class="s">(</span><span class="i">@AvailableCommonValences</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1774 1761 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValence</span> + <span class="i">$AdjustedFormalCharge</span> - <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span>
|
|
|
1775 1762
|
|
|
1776 1763 <span class="k">if</span> <span class="s">(</span><span class="i">$PotentialTotalValence</span> < <span class="n">0</span> || <span class="i">$PotentialTotalValence</span> >= <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1777 1764 <span class="k">last</span> <span class="j">VALENCE</span><span class="sc">;</span>
|
|
|
1778 1765 <span class="s">}</span>
|
|
|
1779 1766 <span class="s">}</span>
|
|
|
1780 1767 <span class="s">}</span>
|
|
|
1781 1768
|
|
|
1782 1769 <span class="k">return</span> <span class="i">$PotentialTotalValence</span> > <span class="n">0</span> ? <span class="i">$PotentialTotalValence</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1783 1770 <span class="s">}</span>
|
|
|
1784 1771
|
|
|
1785 1772 <span class="c"># Adjust sign of the formal charge for potential total common valence calculation</span>
|
|
|
1786 1773 <span class="c"># used during internal valence model to figure out number of implicit hydrogens.</span>
|
|
|
1787 1774 <span class="c">#</span>
|
|
|
1788 <a name="_GetFormalChargeAdjustedForInternalValenceModel-"></a>1775 <span class="k">sub </span><span class="m">_GetFormalChargeAdjustedForInternalValenceModel</span> <span class="s">{</span>
|
|
|
1789 1776 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1790 1777 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$GroupNumber</span><span class="cm">,</span> <span class="i">$SwitchSign</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1791 1778
|
|
|
1792 1779 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1793 1780 <span class="k">if</span> <span class="s">(</span><span class="i">$FormalCharge</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1794 1781 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1795 1782 <span class="s">}</span>
|
|
|
1796 1783
|
|
|
1797 1784 <span class="i">$GroupNumber</span> = <span class="i">$This</span><span class="i">->GetGroupNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1798 1785 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$GroupNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1799 1786 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span>
|
|
|
1800 1787 <span class="s">}</span>
|
|
|
1801 1788
|
|
|
1802 1789 <span class="c"># Group numbers > 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He)</span>
|
|
|
1803 1790 <span class="c">#</span>
|
|
|
1804 1791 <span class="c"># Formal charge sign is not adjusted. Positive and negative values result in the</span>
|
|
|
1805 1792 <span class="c"># increase and decrease of valence.</span>
|
|
|
1806 1793 <span class="c">#</span>
|
|
|
1807 1794 <span class="c"># Group 14 containing C, Si, Ge, Sn, Pb...</span>
|
|
|
1808 1795 <span class="c">#</span>
|
|
|
1809 1796 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
|
|
|
1810 1797 <span class="c"># values result in the decrease of valence.</span>
|
|
|
1811 1798 <span class="c">#</span>
|
|
|
1812 1799 <span class="c"># Group 13 containing B, Al, Ga, In, Tl...</span>
|
|
|
1813 1800 <span class="c">#</span>
|
|
|
1814 1801 <span class="c"># Formal charge sign is always reversed. Positive and negative values result in the</span>
|
|
|
1815 1802 <span class="c"># decrease and increase of valence.</span>
|
|
|
1816 1803 <span class="c">#</span>
|
|
|
1817 1804 <span class="c"># Groups 1 (H) through 12 (Zn)...</span>
|
|
|
1818 1805 <span class="c">#</span>
|
|
|
1819 1806 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
|
|
|
1820 1807 <span class="c"># values result in the decrease of valence.</span>
|
|
|
1821 1808 <span class="c">#</span>
|
|
|
1822 1809 <span class="c"># Lanthanides and actinides...</span>
|
|
|
1823 1810 <span class="c">#</span>
|
|
|
1824 1811 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
|
|
|
1825 1812 <span class="c"># values result in the decrease of valence.</span>
|
|
|
1826 1813 <span class="c">#</span>
|
|
|
1827 1814
|
|
|
1828 1815 <span class="i">$SwitchSign</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1829 1816 <span class="k">if</span> <span class="s">(</span><span class="k">length</span> <span class="i">$GroupNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1830 1817 <span class="j">GROUPNUMBER:</span> <span class="s">{</span>
|
|
|
1831 1818 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> > <span class="n">14</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1832 1819 <span class="c"># Groups on the right side of C group in the periodic table...</span>
|
|
|
1833 1820 <span class="i">$SwitchSign</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1834 1821 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span>
|
|
|
1835 1822 <span class="s">}</span>
|
|
|
1836 1823 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> == <span class="n">14</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1837 1824 <span class="c"># Group containing C, Si, Ge, Sn, Pb...</span>
|
|
|
1838 1825 <span class="i">$SwitchSign</span> = <span class="s">(</span><span class="i">$FormalCharge</span> > <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1839 1826 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span>
|
|
|
1840 1827 <span class="s">}</span>
|
|
|
1841 1828 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> == <span class="n">13</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1842 1829 <span class="c"># Group containing B, Al, Ga, In, Tl...</span>
|
|
|
1843 1830 <span class="i">$SwitchSign</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
1844 1831 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span>
|
|
|
1845 1832 <span class="s">}</span>
|
|
|
1846 1833 <span class="c"># Groups 1 (H) through 12 (Zn)...</span>
|
|
|
1847 1834 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> >=<span class="n">1</span> && <span class="i">$GroupNumber</span> <= <span class="n">12</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1848 1835 <span class="c"># Groups 1 (H) through 12 (Zn)...</span>
|
|
|
1849 1836 <span class="i">$SwitchSign</span> = <span class="s">(</span><span class="i">$FormalCharge</span> > <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1850 1837 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span>
|
|
|
1851 1838 <span class="s">}</span>
|
|
|
1852 1839 <span class="s">}</span>
|
|
|
1853 1840 <span class="s">}</span>
|
|
|
1854 1841 <span class="k">else</span> <span class="s">{</span>
|
|
|
1855 1842 <span class="c"># Lanthanides and actinides...</span>
|
|
|
1856 1843 <span class="i">$SwitchSign</span> = <span class="s">(</span><span class="i">$FormalCharge</span> > <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1857 1844 <span class="s">}</span>
|
|
|
1858 1845
|
|
|
1859 1846 <span class="k">if</span> <span class="s">(</span><span class="i">$SwitchSign</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1860 1847 <span class="i">$FormalCharge</span> *= <span class="n">-1.0</span><span class="sc">;</span>
|
|
|
1861 1848 <span class="s">}</span>
|
|
|
1862 1849
|
|
|
1863 1850 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span>
|
|
|
1864 1851 <span class="s">}</span>
|
|
|
1865 1852
|
|
|
1866 1853 <span class="c"># Get lowest common valence...</span>
|
|
|
1867 <a name="GetLowestCommonValence-"></a>1854 <span class="k">sub </span><span class="m">GetLowestCommonValence</span> <span class="s">{</span>
|
|
|
1868 1855 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1869 1856
|
|
|
1870 1857 <span class="c"># Is LowestCommonValence property explicitly set?</span>
|
|
|
1871 1858 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'LowestCommonValence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1872 1859 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'LowestCommonValence'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1873 1860 <span class="s">}</span>
|
|
|
1874 1861 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$LowestCommonValence</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1875 1862
|
|
|
1876 1863 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
1877 1864 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1878 1865 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1879 1866 <span class="s">}</span>
|
|
|
1880 1867 <span class="c"># Any need to differentiate between internal and other valence models...</span>
|
|
|
1881 1868
|
|
|
1882 1869 <span class="c"># LowestCommonValence is not set for all elements...</span>
|
|
|
1883 1870 <span class="i">$LowestCommonValence</span> = <span class="i">PeriodicTable::GetElementLowestCommonValence</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1884 1871 <span class="k">if</span> <span class="s">(</span>!<span class="i">$LowestCommonValence</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1885 1872 <span class="i">$LowestCommonValence</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
1886 1873 <span class="s">}</span>
|
|
|
1887 1874
|
|
|
1888 1875 <span class="k">return</span> <span class="i">$LowestCommonValence</span><span class="sc">;</span>
|
|
|
1889 1876 <span class="s">}</span>
|
|
|
1890 1877
|
|
|
1891 1878 <span class="c"># Get highest common valence...</span>
|
|
|
1892 <a name="GetHighestCommonValence-"></a>1879 <span class="k">sub </span><span class="m">GetHighestCommonValence</span> <span class="s">{</span>
|
|
|
1893 1880 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1894 1881
|
|
|
1895 1882 <span class="c"># Is HighestCommonValence property explicitly set?</span>
|
|
|
1896 1883 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'HighestCommonValence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1897 1884 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'HighestCommonValence'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1898 1885 <span class="s">}</span>
|
|
|
1899 1886 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$HighestCommonValence</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1900 1887
|
|
|
1901 1888 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
1902 1889 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1903 1890 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1904 1891 <span class="s">}</span>
|
|
|
1905 1892
|
|
|
1906 1893 <span class="c"># Any need to differentiate between internal and other valence models...</span>
|
|
|
1907 1894
|
|
|
1908 1895 <span class="c"># HighestCommonValence is not set for all elements...</span>
|
|
|
1909 1896 <span class="i">$HighestCommonValence</span> = <span class="i">PeriodicTable::GetElementHighestCommonValence</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1910 1897 <span class="k">if</span> <span class="s">(</span>!<span class="i">$HighestCommonValence</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1911 1898 <span class="i">$HighestCommonValence</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
1912 1899 <span class="s">}</span>
|
|
|
1913 1900
|
|
|
1914 1901 <span class="k">return</span> <span class="i">$HighestCommonValence</span><span class="sc">;</span>
|
|
|
1915 1902 <span class="s">}</span>
|
|
|
1916 1903
|
|
|
1917 1904 <span class="c"># Get valence electrons...</span>
|
|
|
1918 <a name="GetValenceElectrons-"></a>1905 <span class="k">sub </span><span class="m">GetValenceElectrons</span> <span class="s">{</span>
|
|
|
1919 1906 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1920 1907
|
|
|
1921 1908 <span class="c"># Is ValenceElectrons property explicitly set?</span>
|
|
|
1922 1909 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1923 1910 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceElectrons'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1924 1911 <span class="s">}</span>
|
|
|
1925 1912 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$ValenceElectrons</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1926 1913
|
|
|
1927 1914 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
1928 1915 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1929 1916 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1930 1917 <span class="s">}</span>
|
|
|
1931 1918
|
|
|
1932 1919 <span class="i">$ValenceElectrons</span> = <span class="i">PeriodicTable::GetElementValenceElectrons</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
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|
|
1933 1920
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|
1934 1921 <span class="k">return</span> <span class="i">$ValenceElectrons</span><span class="sc">;</span>
|
|
|
1935 1922 <span class="s">}</span>
|
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|
1936 1923
|
|
|
1937 1924 <span class="c"># Add hydrogens to specified atom in molecule and return number of hydrogens added:</span>
|
|
|
1938 1925 <span class="c">#</span>
|
|
|
1939 1926 <span class="c"># o HydrogensToAdd = ImplicitHydrogenCount - ExplicitHydrogenCount</span>
|
|
|
1940 1927 <span class="c">#</span>
|
|
|
1941 1928 <span class="c"># o XYZ are set to ZeroVector</span>
|
|
|
1942 1929 <span class="c">#</span>
|
|
|
1943 <a name="AddHydrogens-"></a>1930 <span class="k">sub </span><span class="m">AddHydrogens</span> <span class="s">{</span>
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|
|
1944 1931 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
|
1945 1932
|
|
|
1946 1933 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1947 1934 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1948 1935 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1949 1936 <span class="s">}</span>
|
|
|
1950 1937 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1951 1938 <span class="i">$HydrogenPositionsWarning</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
1952 1939 <span class="s">}</span>
|
|
|
1953 1940 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1954 1941 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddHydrogens: The current release of MayaChemTools doesn't assign any hydrogen positions..."</span><span class="sc">;</span>
|
|
|
1955 1942 <span class="s">}</span>
|
|
|
1956 1943
|
|
|
1957 1944 <span class="c"># Is it an element symbol?</span>
|
|
|
1958 1945 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1959 1946 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1960 1947 <span class="s">}</span>
|
|
|
1961 1948
|
|
|
1962 1949 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$HydrogensAdded</span><span class="cm">,</span> <span class="i">$HydrogensToAdd</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1963 1950
|
|
|
1964 1951 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1965 1952 <span class="i">$HydrogensAdded</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1966 1953 <span class="i">$HydrogensToAdd</span> = <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1967 1954 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogensToAdd</span> <= <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1968 1955 <span class="k">return</span> <span class="i">$HydrogensAdded</span><span class="sc">;</span>
|
|
|
1969 1956 <span class="s">}</span>
|
|
|
1970 1957
|
|
|
1971 1958 <span class="k">my</span><span class="s">(</span><span class="i">$Count</span><span class="cm">,</span> <span class="i">$Hydrogen</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1972 1959
|
|
|
1973 1960 <span class="k">for</span> <span class="i">$Count</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$HydrogensToAdd</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1974 1961 <span class="i">$HydrogensAdded</span>++<span class="sc">;</span>
|
|
|
1975 1962
|
|
|
1976 1963 <span class="i">$Hydrogen</span> = <span class="i">$Molecule</span><span class="i">->NewAtom</span><span class="s">(</span><span class="q">'AtomSymbol'</span> <span class="cm">=></span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'XYZ'</span> <span class="cm">=></span> <span class="s">[</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1977 1964 <span class="i">$Molecule</span><span class="i">->NewBond</span><span class="s">(</span><span class="q">'Atoms'</span> <span class="cm">=></span> <span class="s">[</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Hydrogen</span><span class="s">]</span><span class="cm">,</span> <span class="q">'BondOrder'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1978 1965 <span class="s">}</span>
|
|
|
1979 1966
|
|
|
1980 1967 <span class="k">return</span> <span class="i">$HydrogensAdded</span><span class="sc">;</span>
|
|
|
1981 1968 <span class="s">}</span>
|
|
|
1982 1969
|
|
|
1983 1970 <span class="c"># Delete hydrogens attached to atom in molecule and return total number of hydrogens deleted...</span>
|
|
|
1984 <a name="DeleteHydrogens-"></a>1971 <span class="k">sub </span><span class="m">DeleteHydrogens</span> <span class="s">{</span>
|
|
|
1985 1972 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1986 1973
|
|
|
1987 1974 <span class="c"># Is this atom in a molecule?</span>
|
|
|
1988 1975 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1989 1976 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1990 1977 <span class="s">}</span>
|
|
|
1991 1978
|
|
|
1992 1979 <span class="c"># Is it an element symbol?</span>
|
|
|
1993 1980 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1994 1981 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1995 1982 <span class="s">}</span>
|
|
|
1996 1983
|
|
|
1997 1984 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">$HydrogensDeleted</span><span class="cm">,</span> <span class="i">@Neighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1998 1985
|
|
|
1999 1986 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2000 1987 <span class="i">$HydrogensDeleted</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2001 1988 <span class="i">@Neighbors</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2002 1989
|
|
|
2003 1990 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">@Neighbors</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2004 1991 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Neighbor</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2005 1992 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
|
|
|
2006 1993 <span class="s">}</span>
|
|
|
2007 1994 <span class="i">$Molecule</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$Neighbor</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2008 1995 <span class="i">$HydrogensDeleted</span>++<span class="sc">;</span>
|
|
|
2009 1996 <span class="s">}</span>
|
|
|
2010 1997
|
|
|
2011 1998 <span class="k">return</span> <span class="i">$HydrogensDeleted</span><span class="sc">;</span>
|
|
|
2012 1999 <span class="s">}</span>
|
|
|
2013 2000
|
|
|
2014 2001 <span class="c"># Copy atom and all its associated data...</span>
|
|
|
2015 <a name="Copy-"></a>2002 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span>
|
|
|
2016 2003 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2017 2004 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2018 2005
|
|
|
2019 2006 <span class="i">$Atom</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2020 2007
|
|
|
2021 2008 <span class="k">return</span> <span class="i">$Atom</span><span class="sc">;</span>
|
|
|
2022 2009 <span class="s">}</span>
|
|
|
2023 2010
|
|
|
2024 2011 <span class="c"># Get atomic invariant value...</span>
|
|
|
2025 2012 <span class="c">#</span>
|
|
|
2026 <a name="GetAtomicInvariantValue-"></a>2013 <span class="k">sub </span><span class="m">GetAtomicInvariantValue</span> <span class="s">{</span>
|
|
|
2027 2014 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2028 2015 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2029 2016
|
|
|
2030 2017 <span class="i">$Value</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
2031 2018
|
|
|
2032 2019 <span class="j">ATOMICVARIANT:</span> <span class="s">{</span>
|
|
|
2033 2020 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AS|AtomSymbol|ElementSymbol)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2034 2021 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2035 2022 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2036 2023 <span class="s">}</span>
|
|
|
2037 2024 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(X|NumOfNonHydrogenAtomNeighbors|NumOfHeavyAtomNeighbors)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2038 2025 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2039 2026 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2040 2027 <span class="s">}</span>
|
|
|
2041 2028 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(BO|SumOfBondOrdersToNonHydrogenAtoms|SumOfBondOrdersToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2042 2029 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2043 2030 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2044 2031 <span class="s">}</span>
|
|
|
2045 2032 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(LBO|LargestBondOrderToNonHydrogenAtoms|LargestBondOrderToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2046 2033 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2047 2034 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2048 2035 <span class="s">}</span>
|
|
|
2049 2036 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(H|NumOfImplicitAndExplicitHydrogens)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2050 2037 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2051 2038 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2052 2039 <span class="s">}</span>
|
|
|
2053 2040 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(SB|NumOfSingleBondsToNonHydrogenAtoms|NumOfSingleBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2054 2041 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2055 2042 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2056 2043 <span class="s">}</span>
|
|
|
2057 2044 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(DB|NumOfDoubleBondsToNonHydrogenAtoms|NumOfDoubleBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2058 2045 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2059 2046 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2060 2047 <span class="s">}</span>
|
|
|
2061 2048 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(TB|NumOfTripleBondsToNonHydrogenAtoms|NumOfTripleBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2062 2049 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfTripleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2063 2050 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2064 2051 <span class="s">}</span>
|
|
|
2065 2052 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AB|NumOfAromaticBondsToNonHydrogenAtoms|NumOfAromaticBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2066 2053 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2067 2054 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2068 2055 <span class="s">}</span>
|
|
|
2069 2056 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(FC|FormalCharge)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2070 2057 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2071 2058 <span class="i">$Value</span> = <span class="k">defined</span> <span class="i">$Value</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2072 2059 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2073 2060 <span class="s">}</span>
|
|
|
2074 2061 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(T|TotalNumOfAtomNeighbors)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2075 2062 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2076 2063 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2077 2064 <span class="s">}</span>
|
|
|
2078 2065 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(TSB|TotalNumOfSingleBonds)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2079 2066 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2080 2067 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2081 2068 <span class="s">}</span>
|
|
|
2082 2069 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(Ar|Aromatic)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2083 2070 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2084 2071 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2085 2072 <span class="s">}</span>
|
|
|
2086 2073 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(RA|RingAtom)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2087 2074 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2088 2075 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2089 2076 <span class="s">}</span>
|
|
|
2090 2077 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(Str|Stereochemistry)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2091 2078 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2092 2079 <span class="i">$Value</span>= <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Value</span> =~ <span class="q">/^(R|S)$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
2093 2080 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2094 2081 <span class="s">}</span>
|
|
|
2095 2082 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AN|AtomicNumber)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2096 2083 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2097 2084 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2098 2085 <span class="s">}</span>
|
|
|
2099 2086 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AM|AtomicMass)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2100 2087 <span class="i">$Value</span> = <span class="i">round</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="n">4</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
|
|
|
2101 2088 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2102 2089 <span class="s">}</span>
|
|
|
2103 2090 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(MN|MassNumber)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2104 2091 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2105 2092 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2106 2093 <span class="s">}</span>
|
|
|
2107 2094 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(SM|SpinMultiplicity)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2108 2095 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2109 2096 <span class="i">$Value</span> = <span class="k">defined</span> <span class="i">$Value</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
2110 2097 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
|
|
|
2111 2098 <span class="s">}</span>
|
|
|
2112 2099 <span class="i">$Value</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
2113 2100 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetAtomicInvariantValue: Unknown atomic invariant $AtomicInvariant..."</span><span class="sc">;</span>
|
|
|
2114 2101 <span class="s">}</span>
|
|
|
2115 2102
|
|
|
2116 2103 <span class="k">return</span> <span class="i">$Value</span><span class="sc">;</span>
|
|
|
2117 2104 <span class="s">}</span>
|
|
|
2118 2105
|
|
|
2119 2106 <span class="c"># Get period number of the atom..</span>
|
|
|
2120 2107 <span class="c">#</span>
|
|
|
2121 <a name="GetPeriodNumber-"></a>2108 <span class="k">sub </span><span class="m">GetPeriodNumber</span> <span class="s">{</span>
|
|
|
2122 2109 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2123 2110
|
|
|
2124 2111 <span class="c"># Is PeriodNumber property explicitly set?</span>
|
|
|
2125 2112 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'PeriodNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2126 2113 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'PeriodNumber'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2127 2114 <span class="s">}</span>
|
|
|
2128 2115 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$PeriodNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2129 2116
|
|
|
2130 2117 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
2131 2118 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2132 2119 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2133 2120 <span class="s">}</span>
|
|
|
2134 2121
|
|
|
2135 2122 <span class="i">$PeriodNumber</span> = <span class="i">PeriodicTable::GetElementPeriodNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2136 2123
|
|
|
2137 2124 <span class="k">return</span> <span class="i">$PeriodNumber</span><span class="sc">;</span>
|
|
|
2138 2125 <span class="s">}</span>
|
|
|
2139 2126
|
|
|
2140 2127 <span class="c"># Get group number of the atom..</span>
|
|
|
2141 2128 <span class="c">#</span>
|
|
|
2142 <a name="GetGroupNumber-"></a>2129 <span class="k">sub </span><span class="m">GetGroupNumber</span> <span class="s">{</span>
|
|
|
2143 2130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2144 2131
|
|
|
2145 2132 <span class="c"># Is GroupNumber property explicitly set?</span>
|
|
|
2146 2133 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'GroupNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2147 2134 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'GroupNumber'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2148 2135 <span class="s">}</span>
|
|
|
2149 2136 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$GroupNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2150 2137
|
|
|
2151 2138 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
2152 2139 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2153 2140 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2154 2141 <span class="s">}</span>
|
|
|
2155 2142
|
|
|
2156 2143 <span class="i">$GroupNumber</span> = <span class="i">PeriodicTable::GetElementGroupNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2157 2144
|
|
|
2158 2145 <span class="k">return</span> <span class="i">$GroupNumber</span><span class="sc">;</span>
|
|
|
2159 2146 <span class="s">}</span>
|
|
|
2160 2147
|
|
|
2161 2148 <span class="c"># Is it a specified topological pharmacophore atom type?</span>
|
|
|
2162 2149 <span class="c">#</span>
|
|
|
2163 <a name="IsTopologicalPharmacophoreType-"></a>2150 <span class="k">sub </span><span class="m">IsTopologicalPharmacophoreType</span> <span class="s">{</span>
|
|
|
2164 2151 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2165 2152
|
|
|
2166 2153 <span class="k">return</span> <span class="i">$This</span><span class="i">->_IsFunctionalClassType</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2167 2154 <span class="s">}</span>
|
|
|
2168 2155
|
|
|
2169 2156 <span class="c"># Is it a specified functional class atom type?</span>
|
|
|
2170 2157 <span class="c">#</span>
|
|
|
2171 <a name="IsFunctionalClassType-"></a>2158 <span class="k">sub </span><span class="m">IsFunctionalClassType</span> <span class="s">{</span>
|
|
|
2172 2159 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2173 2160
|
|
|
2174 2161 <span class="k">return</span> <span class="i">$This</span><span class="i">->_IsFunctionalClassType</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2175 2162 <span class="s">}</span>
|
|
|
2176 2163
|
|
|
2177 2164 <span class="c"># Is it a specified functional/topological pharmacophore atom type?</span>
|
|
|
2178 2165 <span class="c">#</span>
|
|
|
2179 <a name="_IsFunctionalClassType-"></a>2166 <span class="k">sub </span><span class="m">_IsFunctionalClassType</span> <span class="s">{</span>
|
|
|
2180 2167 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2181 2168 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2182 2169
|
|
|
2183 2170 <span class="i">$Value</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2184 2171
|
|
|
2185 2172 <span class="j">TYPE:</span> <span class="s">{</span>
|
|
|
2186 2173 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(HBD|HydrogenBondDonor)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2187 2174 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsHydrogenBondDonor</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2188 2175 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
|
|
|
2189 2176 <span class="s">}</span>
|
|
|
2190 2177 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(HBA|HydrogenBondAcceptor)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2191 2178 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsHydrogenBondAcceptor</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2192 2179 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
|
|
|
2193 2180 <span class="s">}</span>
|
|
|
2194 2181 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(PI|PositivelyIonizable)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2195 2182 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsPositivelyIonizable</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2196 2183 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
|
|
|
2197 2184 <span class="s">}</span>
|
|
|
2198 2185 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(NI|NegativelyIonizable)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2199 2186 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsNegativelyIonizable</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2200 2187 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
|
|
|
2201 2188 <span class="s">}</span>
|
|
|
2202 2189 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(H|Hydrophobic)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2203 2190 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsHydrophobic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2204 2191 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
|
|
|
2205 2192 <span class="s">}</span>
|
|
|
2206 2193 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(Ar|Aromatic)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2207 2194 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2208 2195 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
|
|
|
2209 2196 <span class="s">}</span>
|
|
|
2210 2197 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(Hal|Halogen)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2211 2198 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsHalogen</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2212 2199 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
|
|
|
2213 2200 <span class="s">}</span>
|
|
|
2214 2201 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(RA|RingAtom)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2215 2202 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2216 2203 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
|
|
|
2217 2204 <span class="s">}</span>
|
|
|
2218 2205 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(CA|ChainAtom)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2219 2206 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">->IsNotInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2220 2207 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
|
|
|
2221 2208 <span class="s">}</span>
|
|
|
2222 2209 <span class="i">$Value</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2223 2210 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_IsType: Unknown functional/pharmacohore type $Type..."</span><span class="sc">;</span>
|
|
|
2224 2211 <span class="s">}</span>
|
|
|
2225 2212 <span class="k">return</span> <span class="i">$Value</span><span class="sc">;</span>
|
|
|
2226 2213 <span class="s">}</span>
|
|
|
2227 2214
|
|
|
2228 2215 <span class="c"># Is it a Hydrogen atom?</span>
|
|
|
2229 <a name="IsHydrogen-"></a>2216 <span class="k">sub </span><span class="m">IsHydrogen</span> <span class="s">{</span>
|
|
|
2230 2217 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2231 2218
|
|
|
2232 2219 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</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>
|
|
|
2233 2220 <span class="s">}</span>
|
|
|
2234 2221
|
|
|
2235 2222 <span class="c"># Is it a Carbon atom?</span>
|
|
|
2236 <a name="IsCarbon-"></a>2223 <span class="k">sub </span><span class="m">IsCarbon</span> <span class="s">{</span>
|
|
|
2237 2224 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2238 2225
|
|
|
2239 2226 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</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>
|
|
|
2240 2227 <span class="s">}</span>
|
|
|
2241 2228
|
|
|
2242 2229 <span class="c"># Is it a Nitrogen atom?</span>
|
|
|
2243 <a name="IsNitrogen-"></a>2230 <span class="k">sub </span><span class="m">IsNitrogen</span> <span class="s">{</span>
|
|
|
2244 2231 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2245 2232
|
|
|
2246 2233 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">7</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2247 2234 <span class="s">}</span>
|
|
|
2248 2235
|
|
|
2249 2236 <span class="c"># Is it a Oxygen atom?</span>
|
|
|
2250 <a name="IsOxygen-"></a>2237 <span class="k">sub </span><span class="m">IsOxygen</span> <span class="s">{</span>
|
|
|
2251 2238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2252 2239
|
|
|
2253 2240 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">8</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2254 2241 <span class="s">}</span>
|
|
|
2255 2242
|
|
|
2256 2243 <span class="c"># Is it a Fluorine atom?</span>
|
|
|
2257 <a name="IsFluorine-"></a>2244 <span class="k">sub </span><span class="m">IsFluorine</span> <span class="s">{</span>
|
|
|
2258 2245 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2259 2246
|
|
|
2260 2247 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">9</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2261 2248 <span class="s">}</span>
|
|
|
2262 2249
|
|
|
2263 2250 <span class="c"># Is it a Silicon atom?</span>
|
|
|
2264 <a name="IsSilicon-"></a>2251 <span class="k">sub </span><span class="m">IsSilicon</span> <span class="s">{</span>
|
|
|
2265 2252 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2266 2253
|
|
|
2267 2254 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">14</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2268 2255 <span class="s">}</span>
|
|
|
2269 2256
|
|
|
2270 2257 <span class="c"># Is it a Phosphorus atom?</span>
|
|
|
2271 <a name="IsPhosphorus-"></a>2258 <span class="k">sub </span><span class="m">IsPhosphorus</span> <span class="s">{</span>
|
|
|
2272 2259 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2273 2260
|
|
|
2274 2261 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">15</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2275 2262 <span class="s">}</span>
|
|
|
2276 2263
|
|
|
2277 2264 <span class="c"># Is it a Sulphur atom?</span>
|
|
|
2278 <a name="IsSulphur-"></a>2265 <span class="k">sub </span><span class="m">IsSulphur</span> <span class="s">{</span>
|
|
|
2279 2266 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2280 2267
|
|
|
2281 2268 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsSulfur</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2282 2269 <span class="s">}</span>
|
|
|
2283 2270
|
|
|
2284 2271 <span class="c"># Is it a Sulfur atom?</span>
|
|
|
2285 <a name="IsSulfur-"></a>2272 <span class="k">sub </span><span class="m">IsSulfur</span> <span class="s">{</span>
|
|
|
2286 2273 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2287 2274
|
|
|
2288 2275 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">16</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2289 2276 <span class="s">}</span>
|
|
|
2290 2277
|
|
|
2291 2278 <span class="c"># Is it a Chlorine atom?</span>
|
|
|
2292 <a name="IsChlorine-"></a>2279 <span class="k">sub </span><span class="m">IsChlorine</span> <span class="s">{</span>
|
|
|
2293 2280 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2294 2281
|
|
|
2295 2282 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">17</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2296 2283 <span class="s">}</span>
|
|
|
2297 2284
|
|
|
2298 2285 <span class="c"># Is it a Arsenic atom?</span>
|
|
|
2299 <a name="IsArsenic-"></a>2286 <span class="k">sub </span><span class="m">IsArsenic</span> <span class="s">{</span>
|
|
|
2300 2287 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2301 2288
|
|
|
2302 2289 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">33</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2303 2290 <span class="s">}</span>
|
|
|
2304 2291
|
|
|
2305 2292 <span class="c"># Is it a Selenium atom?</span>
|
|
|
2306 <a name="IsSelenium-"></a>2293 <span class="k">sub </span><span class="m">IsSelenium</span> <span class="s">{</span>
|
|
|
2307 2294 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2308 2295
|
|
|
2309 2296 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">34</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2310 2297 <span class="s">}</span>
|
|
|
2311 2298
|
|
|
2312 2299 <span class="c"># Is it a Bromine atom?</span>
|
|
|
2313 <a name="IsBromine-"></a>2300 <span class="k">sub </span><span class="m">IsBromine</span> <span class="s">{</span>
|
|
|
2314 2301 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2315 2302
|
|
|
2316 2303 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">35</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2317 2304 <span class="s">}</span>
|
|
|
2318 2305
|
|
|
2319 2306 <span class="c"># Is it a Tellurium atom?</span>
|
|
|
2320 <a name="IsTellurium-"></a>2307 <span class="k">sub </span><span class="m">IsTellurium</span> <span class="s">{</span>
|
|
|
2321 2308 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2322 2309
|
|
|
2323 2310 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">52</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2324 2311 <span class="s">}</span>
|
|
|
2325 2312
|
|
|
2326 2313 <span class="c"># Is it a Iodine atom?</span>
|
|
|
2327 <a name="IsIodine-"></a>2314 <span class="k">sub </span><span class="m">IsIodine</span> <span class="s">{</span>
|
|
|
2328 2315 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2329 2316
|
|
|
2330 2317 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">53</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2331 2318 <span class="s">}</span>
|
|
|
2332 2319
|
|
|
2333 2320 <span class="c"># Is it a hetro atom? (N, O, F, P, S, Cl, Br, I)</span>
|
|
|
2334 <a name="IsHeteroAtom-"></a>2321 <span class="k">sub </span><span class="m">IsHeteroAtom</span> <span class="s">{</span>
|
|
|
2335 2322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2336 2323
|
|
|
2337 2324 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8|9|15|16|17|35|53)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2338 2325 <span class="s">}</span>
|
|
|
2339 2326
|
|
|
2340 2327 <span class="c"># Is it a halogen atom? (F, Cl, Br, I)</span>
|
|
|
2341 <a name="IsHalogen-"></a>2328 <span class="k">sub </span><span class="m">IsHalogen</span> <span class="s">{</span>
|
|
|
2342 2329 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2343 2330
|
|
|
2344 2331 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(9|17|35|53)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2345 2332 <span class="s">}</span>
|
|
|
2346 2333
|
|
|
2347 2334 <span class="c"># Is it classified as metallic?</span>
|
|
|
2348 <a name="IsMetallic-"></a>2335 <span class="k">sub </span><span class="m">IsMetallic</span> <span class="s">{</span>
|
|
|
2349 2336 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2350 2337 <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2351 2338
|
|
|
2352 2339 <span class="i">$Classification</span> = <span class="i">PeriodicTable::GetElementClassification</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
2353 2340
|
|
|
2354 2341 <span class="k">return</span> <span class="s">(</span><span class="i">$Classification</span> =~ <span class="q">/^Metallic$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2355 2342 <span class="s">}</span>
|
|
|
2356 2343
|
|
|
2357 2344 <span class="c"># Is it a non carbon or hydrogen atom? (C, H)</span>
|
|
|
2358 <a name="IsNonCarbonOrHydrogen-"></a>2345 <span class="k">sub </span><span class="m">IsNonCarbonOrHydrogen</span> <span class="s">{</span>
|
|
|
2359 2346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2360 2347
|
|
|
2361 2348 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(1|6)$/</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2362 2349 <span class="s">}</span>
|
|
|
2363 2350
|
|
|
2364 2351 <span class="c"># Is it a polar atom? ( N, O, P, S)</span>
|
|
|
2365 <a name="IsPolarAtom-"></a>2352 <span class="k">sub </span><span class="m">IsPolarAtom</span> <span class="s">{</span>
|
|
|
2366 2353 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2367 2354
|
|
|
2368 2355 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8|15|16)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2369 2356 <span class="s">}</span>
|
|
|
2370 2357
|
|
|
2371 2358 <span class="c"># Is it an isotope?</span>
|
|
|
2372 <a name="IsIsotope-"></a>2359 <span class="k">sub </span><span class="m">IsIsotope</span> <span class="s">{</span>
|
|
|
2373 2360 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2374 2361
|
|
|
2375 2362 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
|
|
|
2376 2363 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2377 2364 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2378 2365 <span class="s">}</span>
|
|
|
2379 2366
|
|
|
2380 2367 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2381 2368 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2382 2369 <span class="s">}</span>
|
|
|
2383 2370 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="cm">,</span> <span class="i">$MostAbundantMassNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2384 2371
|
|
|
2385 2372 <span class="i">$MassNumber</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2386 2373 <span class="i">$MostAbundantMassNumber</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2387 2374
|
|
|
2388 2375 <span class="k">return</span> <span class="s">(</span><span class="i">$MassNumber</span> == <span class="i">$MostAbundantMassNumber</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2389 2376 <span class="s">}</span>
|
|
|
2390 2377
|
|
|
2391 2378 <span class="c"># Is it a terminal atom?</span>
|
|
|
2392 <a name="IsTerminal-"></a>2379 <span class="k">sub </span><span class="m">IsTerminal</span> <span class="s">{</span>
|
|
|
2393 2380 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2394 2381
|
|
|
2395 2382 <span class="c"># Is this atom in a molecule?</span>
|
|
|
2396 2383 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2397 2384 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
2398 2385 <span class="s">}</span>
|
|
|
2399 2386
|
|
|
2400 2387 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> <= <span class="n">1</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span>
|
|
|
2401 2388
|
|
|
2402 2389 <span class="s">}</span>
|
|
|
2403 2390
|
|
|
2404 2391 <span class="c"># Is aromatic property set for the atom?</span>
|
|
|
2405 <a name="IsAromatic-"></a>2392 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span>
|
|
|
2406 2393 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2407 2394 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2408 2395
|
|
|
2409 2396 <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>
|
|
|
2410 2397
|
|
|
2411 2398 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span> && <span class="i">$Aromatic</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2412 2399 <span class="s">}</span>
|
|
|
2413 2400
|
|
|
2414 2401 <span class="c"># Is this a hydrogen atom and attached to one of these atoms: N, O, P, S</span>
|
|
|
2415 <a name="IsPolarHydrogen-"></a>2402 <span class="k">sub </span><span class="m">IsPolarHydrogen</span> <span class="s">{</span>
|
|
|
2416 2403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2417 2404
|
|
|
2418 2405 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2419 2406 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2420 2407 <span class="s">}</span>
|
|
|
2421 2408
|
|
|
2422 2409 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2423 2410 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2424 2411 <span class="k">if</span> <span class="s">(</span><span class="i">@Bonds</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2425 2412 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2426 2413 <span class="s">}</span>
|
|
|
2427 2414
|
|
|
2428 2415 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2429 2416 <span class="s">(</span><span class="i">$Bond</span><span class="s">)</span> = <span class="i">@Bonds</span><span class="sc">;</span>
|
|
|
2430 2417 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2431 2418
|
|
|
2432 2419 <span class="k">return</span> <span class="i">$BondedAtom</span><span class="i">->IsPolarAtom</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2433 2420 <span class="s">}</span>
|
|
|
2434 2421
|
|
|
2435 2422 <span class="c"># Is it a hydrogen bond donor atom?</span>
|
|
|
2436 2423 <span class="c">#</span>
|
|
|
2437 <a name="IsHBondDonor-"></a>2424 <span class="k">sub </span><span class="m">IsHBondDonor</span> <span class="s">{</span>
|
|
|
2438 2425 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2439 2426
|
|
|
2440 2427 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsHydrogenBondDonor</span><span class="s">(</span><span class="i">$HydrogenBondsType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2441 2428 <span class="s">}</span>
|
|
|
2442 2429
|
|
|
2443 2430 <span class="c"># The currrent release of MayaChemTools supports identification of two types of</span>
|
|
|
2444 2431 <span class="c"># hydrogen bond donor and acceptor atoms with these names:</span>
|
|
|
2445 2432 <span class="c">#</span>
|
|
|
2446 2433 <span class="c"># HBondsType1 or HydrogenBondsType1</span>
|
|
|
2447 2434 <span class="c"># HBondsType2 or HydrogenBondsType2</span>
|
|
|
2448 2435 <span class="c">#</span>
|
|
|
2449 2436 <span class="c"># The names of these hydrogen bond types are rather arbitrary. However, their</span>
|
|
|
2450 2437 <span class="c"># definitions have specific meaning and are as follows:</span>
|
|
|
2451 2438 <span class="c">#</span>
|
|
|
2452 2439 <span class="c"># HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</span>
|
|
|
2453 2440 <span class="c"># . Donor: NH, NH2, NH3, OH - Any N and O with available H</span>
|
|
|
2454 2441 <span class="c"># . Acceptor: N[!H], O - Any N without available H and any O</span>
|
|
|
2455 2442 <span class="c">#</span>
|
|
|
2456 2443 <span class="c"># HydrogenBondsType2 [ Ref 91 ]:</span>
|
|
|
2457 2444 <span class="c"># . Donor: NH, NH2, NH3, OH - Any N and O with availabe H</span>
|
|
|
2458 2445 <span class="c"># . Acceptor: N, O - Any N and O</span>
|
|
|
2459 2446 <span class="c">#</span>
|
|
|
2460 2447 <span class="c"># Note:</span>
|
|
|
2461 2448 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span>
|
|
|
2462 2449 <span class="c">#</span>
|
|
|
2463 2450
|
|
|
2464 2451 <span class="c"># Is it a hydrogen bond donor atom?</span>
|
|
|
2465 2452 <span class="c">#</span>
|
|
|
2466 2453 <span class="c"># The currrent release of MayaChemTools supports identification of two types of</span>
|
|
|
2467 <a name="IsHydrogenBondDonor-"></a>2454 <span class="k">sub </span><span class="m">IsHydrogenBondDonor</span> <span class="s">{</span>
|
|
|
2468 2455 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2469 2456 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2470 2457
|
|
|
2471 2458 <span class="i">$HydrogenBondsType</span> = <span class="k">defined</span> <span class="i">$HydrogenBondsType</span> ? <span class="i">$HydrogenBondsType</span> <span class="co">:</span> <span class="q">'HBondsType1'</span><span class="sc">;</span>
|
|
|
2472 2459 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2473 2460
|
|
|
2474 2461 <span class="j">HYDROGENBONDSTYPE:</span> <span class="s">{</span>
|
|
|
2475 2462
|
|
|
2476 2463 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType1|HydrogenBondsType1)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2477 2464 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType1</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2478 2465 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span>
|
|
|
2479 2466 <span class="s">}</span>
|
|
|
2480 2467
|
|
|
2481 2468 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2482 2469 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2483 2470 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span>
|
|
|
2484 2471 <span class="s">}</span>
|
|
|
2485 2472
|
|
|
2486 2473 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2487 2474 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->IsHydrogenBondDonor: The current release of MayaChemTools doesn't support specified value, $HydrogenBondsType, for HydrogenBondsType. Valid values: HBondsType1, HydrogenBondsType1, HBondsType2 HydrogenBondsType2 ..."</span><span class="sc">;</span>
|
|
|
2488 2475 <span class="s">}</span>
|
|
|
2489 2476
|
|
|
2490 2477 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
2491 2478 <span class="s">}</span>
|
|
|
2492 2479
|
|
|
2493 2480 <span class="c"># Is it a MayaChemTools HBondType1 hydrogen bond donor atom?</span>
|
|
|
2494 2481 <span class="c">#</span>
|
|
|
2495 <a name="_IsHydrogenBondDonorOfType1-"></a>2482 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType1</span> <span class="s">{</span>
|
|
|
2496 2483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2497 2484
|
|
|
2498 2485 <span class="k">return</span> <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType1OrType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2499 2486 <span class="s">}</span>
|
|
|
2500 2487
|
|
|
2501 2488 <span class="c"># Is it a MayaChemTools HBondType2 hydrogen bond donor atom?</span>
|
|
|
2502 2489 <span class="c">#</span>
|
|
|
2503 <a name="_IsHydrogenBondDonorOfType2-"></a>2490 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType2</span> <span class="s">{</span>
|
|
|
2504 2491 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2505 2492
|
|
|
2506 2493 <span class="k">return</span> <span class="i">$This</span><span class="i">->_IsHydrogenBondDonorOfType1OrType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2507 2494 <span class="s">}</span>
|
|
|
2508 2495
|
|
|
2509 2496 <span class="c"># Is it a hydrogen bond donor atom of MayaChemTools Type1 or Type2?</span>
|
|
|
2510 2497 <span class="c">#</span>
|
|
|
2511 2498 <span class="c"># HydrogenBondDonor definition [ Ref 60-61, Ref 65-66, Ref 91 ]: NH, NH2, OH</span>
|
|
|
2512 2499 <span class="c">#</span>
|
|
|
2513 2500 <span class="c"># In other words:</span>
|
|
|
2514 2501 <span class="c"># . NH, NH2 - Nitrogen atom with available hydrogen</span>
|
|
|
2515 2502 <span class="c"># . OH - Oxygen atom with avilable hydrogen</span>
|
|
|
2516 2503 <span class="c">#</span>
|
|
|
2517 <a name="_IsHydrogenBondDonorOfType1OrType2-"></a>2504 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType1OrType2</span> <span class="s">{</span>
|
|
|
2518 2505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2519 2506
|
|
|
2520 2507 <span class="c"># Is this atom in a molecule?</span>
|
|
|
2521 2508 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
2522 2509 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2523 2510 <span class="s">}</span>
|
|
|
2524 2511
|
|
|
2525 2512 <span class="c"># Is it N or O?</span>
|
|
|
2526 2513 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(7|8)$/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2527 2514 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2528 2515 <span class="s">}</span>
|
|
|
2529 2516
|
|
|
2530 2517 <span class="c"># Any explicitly attached hydrogens?</span>
|
|
|
2531 2518 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2532 2519 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2533 2520 <span class="s">}</span>
|
|
|
2534 2521
|
|
|
2535 2522 <span class="c"># Any missing hydrogens?</span>
|
|
|
2536 2523 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2537 2524 <span class="s">}</span>
|
|
|
2538 2525
|
|
|
2539 2526 <span class="c"># Is it a hydrogen bond acceptor atom?</span>
|
|
|
2540 2527 <span class="c">#</span>
|
|
|
2541 <a name="IsHBondAcceptor-"></a>2528 <span class="k">sub </span><span class="m">IsHBondAcceptor</span> <span class="s">{</span>
|
|
|
2542 2529 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2543 2530
|
|
|
2544 2531 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsHydrogenBondAcceptor</span><span class="s">(</span><span class="i">$HydrogenBondsType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2545 2532 <span class="s">}</span>
|
|
|
2546 2533
|
|
|
2547 2534 <span class="c"># Is it a hydrogen bond acceptor atom?</span>
|
|
|
2548 2535 <span class="c">#</span>
|
|
|
2549 <a name="IsHydrogenBondAcceptor-"></a>2536 <span class="k">sub </span><span class="m">IsHydrogenBondAcceptor</span> <span class="s">{</span>
|
|
|
2550 2537 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2551 2538 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2552 2539
|
|
|
2553 2540 <span class="i">$HydrogenBondsType</span> = <span class="k">defined</span> <span class="i">$HydrogenBondsType</span> ? <span class="i">$HydrogenBondsType</span> <span class="co">:</span> <span class="q">'HBondsType1'</span><span class="sc">;</span>
|
|
|
2554 2541 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2555 2542
|
|
|
2556 2543 <span class="j">HYDROGENBONDSTYPE:</span> <span class="s">{</span>
|
|
|
2557 2544
|
|
|
2558 2545 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType1|HydrogenBondsType1)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2559 2546 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondAcceptorOfType1</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2560 2547 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span>
|
|
|
2561 2548 <span class="s">}</span>
|
|
|
2562 2549
|
|
|
2563 2550 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2564 2551 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_IsHydrogenBondAcceptorOfType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2565 2552 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span>
|
|
|
2566 2553 <span class="s">}</span>
|
|
|
2567 2554
|
|
|
2568 2555 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2569 2556 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->IsHydrogenBondAcceptor: The current release of MayaChemTools doesn't support specified value, $HydrogenBondsType, for HydrogenBondsType. Valid values: HBondsType1, HydrogenBondsType1, HBondsType2 HydrogenBondsType2 ..."</span><span class="sc">;</span>
|
|
|
2570 2557 <span class="s">}</span>
|
|
|
2571 2558
|
|
|
2572 2559 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
2573 2560 <span class="s">}</span>
|
|
|
2574 2561
|
|
|
2575 2562 <span class="c"># Is it a MayaChemTools HBondType1 hydrogen bond acceptor atom?</span>
|
|
|
2576 2563 <span class="c">#</span>
|
|
|
2577 2564 <span class="c"># HydrogenBondAcceptor definition [ Ref 60-61, Ref 65-66 ]: N[!H], O</span>
|
|
|
2578 2565 <span class="c">#</span>
|
|
|
2579 2566 <span class="c"># In other words:</span>
|
|
|
2580 2567 <span class="c"># . N[!H] - Nitrogen atom with no hydrogen</span>
|
|
|
2581 2568 <span class="c"># . O - Oxygen atom</span>
|
|
|
2582 2569 <span class="c">#</span>
|
|
|
2583 <a name="_IsHydrogenBondAcceptorOfType1-"></a>2570 <span class="k">sub </span><span class="m">_IsHydrogenBondAcceptorOfType1</span> <span class="s">{</span>
|
|
|
2584 2571 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2585 2572
|
|
|
2586 2573 <span class="c"># Is this atom in a molecule?</span>
|
|
|
2587 2574 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
2588 2575 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2589 2576 <span class="s">}</span>
|
|
|
2590 2577
|
|
|
2591 2578 <span class="c"># Is it N or O?</span>
|
|
|
2592 2579 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(7|8)$/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2593 2580 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2594 2581 <span class="s">}</span>
|
|
|
2595 2582
|
|
|
2596 2583 <span class="c"># Is it O?</span>
|
|
|
2597 2584 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">8</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
2598 2585 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2599 2586 <span class="s">}</span>
|
|
|
2600 2587
|
|
|
2601 2588 <span class="c"># Any explicitly attached hydrogens?</span>
|
|
|
2602 2589 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2603 2590 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2604 2591 <span class="s">}</span>
|
|
|
2605 2592
|
|
|
2606 2593 <span class="c"># Any missing hydrogens?</span>
|
|
|
2607 2594 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2608 2595 <span class="s">}</span>
|
|
|
2609 2596
|
|
|
2610 2597 <span class="c"># Is it a MayaChemTools HBondType2 hydrogen bond acceptor atom?</span>
|
|
|
2611 2598 <span class="c">#</span>
|
|
|
2612 2599 <span class="c"># HydrogenBondAcceptor definition [ Ref 91 ]: N, O</span>
|
|
|
2613 2600 <span class="c">#</span>
|
|
|
2614 2601 <span class="c"># In other words:</span>
|
|
|
2615 2602 <span class="c"># . Any Nitrogen or Oxygen atom</span>
|
|
|
2616 2603 <span class="c">#</span>
|
|
|
2617 2604 <span class="c"># Note:</span>
|
|
|
2618 2605 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span>
|
|
|
2619 2606 <span class="c">#</span>
|
|
|
2620 <a name="_IsHydrogenBondAcceptorOfType2-"></a>2607 <span class="k">sub </span><span class="m">_IsHydrogenBondAcceptorOfType2</span> <span class="s">{</span>
|
|
|
2621 2608 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2622 2609
|
|
|
2623 2610 <span class="c"># Is this atom in a molecule?</span>
|
|
|
2624 2611 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2625 2612 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2626 2613 <span class="s">}</span>
|
|
|
2627 2614
|
|
|
2628 2615 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2629 2616 <span class="s">}</span>
|
|
|
2630 2617
|
|
|
2631 2618 <span class="c"># Is it a positively ionizable atom?</span>
|
|
|
2632 2619 <span class="c">#</span>
|
|
|
2633 2620 <span class="c"># PositivelyIonizable defintion [ Ref 60-61, Ref 65-66 ]: +, NH2</span>
|
|
|
2634 2621 <span class="c">#</span>
|
|
|
2635 2622 <span class="c"># In other words:</span>
|
|
|
2636 2623 <span class="c"># . Any atom with positve formal charge</span>
|
|
|
2637 2624 <span class="c"># . NH2 - Nitogen atom in amino group</span>
|
|
|
2638 2625 <span class="c">#</span>
|
|
|
2639 <a name="IsPositivelyIonizable-"></a>2626 <span class="k">sub </span><span class="m">IsPositivelyIonizable</span> <span class="s">{</span>
|
|
|
2640 2627 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2641 2628 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2642 2629
|
|
|
2643 2630 <span class="c"># Is this atom in a molecule?</span>
|
|
|
2644 2631 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
2645 2632 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2646 2633 <span class="s">}</span>
|
|
|
2647 2634
|
|
|
2648 2635 <span class="c"># Any explicit positive formal charge?</span>
|
|
|
2649 2636 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2650 2637 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> && <span class="i">$FormalCharge</span> > <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2651 2638 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2652 2639 <span class="s">}</span>
|
|
|
2653 2640
|
|
|
2654 2641 <span class="c"># Is it N?</span>
|
|
|
2655 2642 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} != <span class="n">7</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
2656 2643 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2657 2644 <span class="s">}</span>
|
|
|
2658 2645
|
|
|
2659 2646 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</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>
|
|
|
2660 2647 <span class="s">}</span>
|
|
|
2661 2648
|
|
|
2662 2649 <span class="c"># Is it a negatively ionizable atom?</span>
|
|
|
2663 2650 <span class="c">#</span>
|
|
|
2664 2651 <span class="c"># NegativelyIonizable definition [ Ref 60-61, Ref 65-66 ]: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
|
|
|
2665 2652 <span class="c">#</span>
|
|
|
2666 2653 <span class="c"># In other words:</span>
|
|
|
2667 2654 <span class="c"># . Any atom with negative formal charge</span>
|
|
|
2668 2655 <span class="c"># . Carbon atom in C(=O)OH group</span>
|
|
|
2669 2656 <span class="c"># . Phosphorous in P(=O)OH group</span>
|
|
|
2670 2657 <span class="c"># . Sulfur atom in S(=O)OH group</span>
|
|
|
2671 2658 <span class="c">#</span>
|
|
|
2672 <a name="IsNegativelyIonizable-"></a>2659 <span class="k">sub </span><span class="m">IsNegativelyIonizable</span> <span class="s">{</span>
|
|
|
2673 2660 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2674 2661 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2675 2662
|
|
|
2676 2663 <span class="c"># Is this atom in a molecule?</span>
|
|
|
2677 2664 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2678 2665 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2679 2666 <span class="s">}</span>
|
|
|
2680 2667
|
|
|
2681 2668 <span class="c"># Any explicit negative formal charge?</span>
|
|
|
2682 2669 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2683 2670 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> && <span class="i">$FormalCharge</span> < <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2684 2671 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2685 2672 <span class="s">}</span>
|
|
|
2686 2673
|
|
|
2687 2674 <span class="c"># Is it C, P or S?</span>
|
|
|
2688 2675 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(6|15|16)$/</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
2689 2676 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2690 2677 <span class="s">}</span>
|
|
|
2691 2678
|
|
|
2692 2679 <span class="c"># Collect oxygens connected to C, P or S with single or double bonds and not connected to</span>
|
|
|
2693 2680 <span class="c"># any other heavy atom...</span>
|
|
|
2694 2681 <span class="k">my</span><span class="s">(</span><span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">$NeighborOxygenBondOrder</span><span class="cm">,</span> <span class="i">$NumOfNeighborOxygensWithSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2695 2682
|
|
|
2696 2683 <span class="i">$NumOfNeighborOxygensWithSingleBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2697 2684
|
|
|
2698 2685 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2699 2686 <span class="c"># Is it an oxygen?</span>
|
|
|
2700 2687 <span class="k">if</span> <span class="s">(</span><span class="i">$Neighbor</span>->{<span class="w">AtomicNumber</span>} != <span class="n">8</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2701 2688 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
|
|
|
2702 2689 <span class="s">}</span>
|
|
|
2703 2690 <span class="c"># Is oxygent connected to only heavy atom?</span>
|
|
|
2704 2691 <span class="k">if</span> <span class="s">(</span><span class="i">$Neighbor</span><span class="i">->GetNumOfHeavyAtomNeighbors</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2705 2692 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
|
|
|
2706 2693 <span class="s">}</span>
|
|
|
2707 2694 <span class="i">$NeighborOxygenBondOrder</span> = <span class="i">$This</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="i">$Neighbor</span><span class="s">)</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2708 2695
|
|
|
2709 2696 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborOxygenBondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2710 2697 <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span>++<span class="sc">;</span>
|
|
|
2711 2698 <span class="s">}</span>
|
|
|
2712 2699 <span class="k">elsif</span> <span class="s">(</span><span class="i">$NeighborOxygenBondOrder</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2713 2700 <span class="i">$NumOfNeighborOxygensWithSingleBonds</span>++<span class="sc">;</span>
|
|
|
2714 2701 <span class="s">}</span>
|
|
|
2715 2702 <span class="s">}</span>
|
|
|
2716 2703 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfNeighborOxygensWithDoubleBonds</span> >= <span class="n">1</span> && <span class="i">$NumOfNeighborOxygensWithSingleBonds</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>
|
|
|
2717 2704 <span class="s">}</span>
|
|
|
2718 2705
|
|
|
2719 2706 <span class="c"># Is it a liphophilic atom?</span>
|
|
|
2720 2707 <span class="c">#</span>
|
|
|
2721 2708 <span class="c"># Lipophilic definition [ Ref 60-61, Ref 65-66 ]: C(C)(C)(C)(C), Cl, Br, I, S(C)(C)</span>
|
|
|
2722 2709 <span class="c">#</span>
|
|
|
2723 2710 <span class="c"># In other words:</span>
|
|
|
2724 2711 <span class="c"># . C(C)(C)(C)(C) - Carbon atom connected to only other carbons</span>
|
|
|
2725 2712 <span class="c"># . Chlorine, Bromine or Iodine atom</span>
|
|
|
2726 2713 <span class="c"># . S(C)(C) - Sulfur connected to two carbons</span>
|
|
|
2727 2714 <span class="c">#</span>
|
|
|
2728 <a name="IsLipophilic-"></a>2715 <span class="k">sub </span><span class="m">IsLipophilic</span> <span class="s">{</span>
|
|
|
2729 2716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2730 2717
|
|
|
2731 2718 <span class="c"># Is this atom in a molecule?</span>
|
|
|
2732 2719 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
2733 2720 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2734 2721 <span class="s">}</span>
|
|
|
2735 2722
|
|
|
2736 2723 <span class="c"># Is it Cl, Br, I?</span>
|
|
|
2737 2724 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(17|35|53)$/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2738 2725 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2739 2726 <span class="s">}</span>
|
|
|
2740 2727
|
|
|
2741 2728 <span class="c"># Is it C, S?</span>
|
|
|
2742 2729 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(6|16)$/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2743 2730 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2744 2731 <span class="s">}</span>
|
|
|
2745 2732
|
|
|
2746 2733 <span class="c"># Are all heavy atom neighbors Carbons?</span>
|
|
|
2747 2734 <span class="k">my</span><span class="s">(</span><span class="i">$HeavyAtomNeighbor</span><span class="cm">,</span> <span class="i">@HeavyAtomNeighbors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2748 2735 <span class="i">@HeavyAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2749 2736 <span class="i">@HeavyAtomNeighbors</span> = <span class="i">$This</span><span class="i">->GetHeavyAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2750 2737
|
|
|
2751 2738 <span class="k">for</span> <span class="i">$HeavyAtomNeighbor</span> <span class="s">(</span><span class="i">@HeavyAtomNeighbors</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2752 2739 <span class="k">if</span> <span class="s">(</span><span class="i">$HeavyAtomNeighbor</span>->{<span class="w">AtomicNumber</span>} != <span class="n">6</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2753 2740 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2754 2741 <span class="s">}</span>
|
|
|
2755 2742 <span class="s">}</span>
|
|
|
2756 2743
|
|
|
2757 2744 <span class="c"># Does sulfur has two carbon neighbors?</span>
|
|
|
2758 2745 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">16</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2759 2746 <span class="k">if</span> <span class="s">(</span><span class="i">@HeavyAtomNeighbors</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2760 2747 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2761 2748 <span class="s">}</span>
|
|
|
2762 2749 <span class="s">}</span>
|
|
|
2763 2750 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2764 2751 <span class="s">}</span>
|
|
|
2765 2752
|
|
|
2766 2753 <span class="c"># Is it hydrophobic?</span>
|
|
|
2767 2754 <span class="c">#</span>
|
|
|
2768 <a name="IsHydrophobic-"></a>2755 <span class="k">sub </span><span class="m">IsHydrophobic</span> <span class="s">{</span>
|
|
|
2769 2756 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2770 2757
|
|
|
2771 2758 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsLipophilic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2772 2759 <span class="s">}</span>
|
|
|
2773 2760
|
|
|
2774 2761 <span class="c"># Is it a Nitrogen atom in Guadinium group?</span>
|
|
|
2775 2762 <span class="c">#</span>
|
|
|
2776 <a name="IsGuadiniumNitrogen-"></a>2763 <span class="k">sub </span><span class="m">IsGuadiniumNitrogen</span> <span class="s">{</span>
|
|
|
2777 2764 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2778 2765
|
|
|
2779 2766 <span class="c"># Is it Nitrogen?</span>
|
|
|
2780 2767 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2781 2768 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2782 2769 <span class="s">}</span>
|
|
|
2783 2770
|
|
|
2784 2771 <span class="c"># Is it connected to a Guadinium Carbon?</span>
|
|
|
2785 2772 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2786 2773
|
|
|
2787 2774 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2788 2775 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->IsGuadiniumCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2789 2776 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2790 2777 <span class="s">}</span>
|
|
|
2791 2778 <span class="s">}</span>
|
|
|
2792 2779
|
|
|
2793 2780 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2794 2781 <span class="s">}</span>
|
|
|
2795 2782
|
|
|
2796 2783 <span class="c"># Is it a Carbon atom in Guadinium group?</span>
|
|
|
2797 2784 <span class="c">#</span>
|
|
|
2798 2785 <span class="c"># Guadinium group definition:</span>
|
|
|
2799 2786 <span class="c">#</span>
|
|
|
2800 2787 <span class="c"># R2N-C(=NR)-(NR2) or R2N-C(=NR2+)-(NR2)</span>
|
|
|
2801 2788 <span class="c">#</span>
|
|
|
2802 2789 <span class="c"># where:</span>
|
|
|
2803 2790 <span class="c"># . R = Hydrogens or group of atoms attached through Carbon</span>
|
|
|
2804 2791 <span class="c"># . Only one of the three Nitrogens has a double bond to Carbon and has optional</span>
|
|
|
2805 2792 <span class="c"># formal charge allowing it to be neutral or charged state</span>
|
|
|
2806 2793 <span class="c">#</span>
|
|
|
2807 <a name="IsGuadiniumCarbon-"></a>2794 <span class="k">sub </span><span class="m">IsGuadiniumCarbon</span> <span class="s">{</span>
|
|
|
2808 2795 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2809 2796
|
|
|
2810 2797 <span class="c"># Is it Carbon?</span>
|
|
|
2811 2798 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2812 2799 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2813 2800 <span class="s">}</span>
|
|
|
2814 2801
|
|
|
2815 2802 <span class="c"># Match atom neighborhood...</span>
|
|
|
2816 2803 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2817 2804
|
|
|
2818 2805 <span class="i">$CentralAtomSpec</span> = <span class="q">'C.X3.BO4'</span><span class="sc">;</span>
|
|
|
2819 2806 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'N.FC0'</span><span class="cm">,</span> <span class="q">'N.FC0'</span><span class="cm">,</span> <span class="q">'N.FC0,N.FC+1'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2820 2807 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2821 2808 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2822 2809
|
|
|
2823 2810 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2824 2811 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2825 2812 <span class="s">}</span>
|
|
|
2826 2813
|
|
|
2827 2814 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2828 2815 <span class="s">}</span>
|
|
|
2829 2816
|
|
|
2830 2817 <span class="c"># Is it a Nitrogen atom in Amide group?</span>
|
|
|
2831 2818 <span class="c">#</span>
|
|
|
2832 <a name="IsAmideNitrogen-"></a>2819 <span class="k">sub </span><span class="m">IsAmideNitrogen</span> <span class="s">{</span>
|
|
|
2833 2820 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2834 2821
|
|
|
2835 2822 <span class="c"># Is it Nitrogen?</span>
|
|
|
2836 2823 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2837 2824 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2838 2825 <span class="s">}</span>
|
|
|
2839 2826
|
|
|
2840 2827 <span class="c"># Is it connected to a Amide Carbon?</span>
|
|
|
2841 2828 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2842 2829
|
|
|
2843 2830 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2844 2831 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->IsAmideCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2845 2832 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2846 2833 <span class="s">}</span>
|
|
|
2847 2834 <span class="s">}</span>
|
|
|
2848 2835
|
|
|
2849 2836 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2850 2837 <span class="s">}</span>
|
|
|
2851 2838
|
|
|
2852 2839 <span class="c"># Is it a Carbon atom in Amide group?</span>
|
|
|
2853 2840 <span class="c">#</span>
|
|
|
2854 2841 <span class="c"># Amide group definition: R-C(=O)-N(-R')-R''</span>
|
|
|
2855 2842 <span class="c">#</span>
|
|
|
2856 2843 <span class="c"># where:</span>
|
|
|
2857 2844 <span class="c"># . R = Hydrogen or groups of atoms attached through Carbon</span>
|
|
|
2858 2845 <span class="c"># . R' = Hydrogens or groups of atoms attached through Carbon or hetro atoms</span>
|
|
|
2859 2846 <span class="c"># . R'' = Hydrogens or groups of atoms attached through Carbon or hetro atoms</span>
|
|
|
2860 2847 <span class="c">#</span>
|
|
|
2861 <a name="IsAmideCarbon-"></a>2848 <span class="k">sub </span><span class="m">IsAmideCarbon</span> <span class="s">{</span>
|
|
|
2862 2849 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2863 2850
|
|
|
2864 2851 <span class="c"># Is this atom in a molecule?</span>
|
|
|
2865 2852 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2866 2853 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2867 2854 <span class="s">}</span>
|
|
|
2868 2855
|
|
|
2869 2856 <span class="c"># Is it Carbon?</span>
|
|
|
2870 2857 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2871 2858 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2872 2859 <span class="s">}</span>
|
|
|
2873 2860
|
|
|
2874 2861 <span class="c"># Match atom neighborhood...</span>
|
|
|
2875 2862 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2876 2863
|
|
|
2877 2864 <span class="i">$CentralAtomSpec</span> = <span class="q">'C.X3.BO4,C.X2.BO3'</span><span class="sc">;</span>
|
|
|
2878 2865 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'N'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2879 2866 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2880 2867 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C'</span><span class="cm">,</span> <span class="q">'C,H,N,O,S,P,F,Cl,Br,I'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2881 2868
|
|
|
2882 2869 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2883 2870 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2884 2871 <span class="s">}</span>
|
|
|
2885 2872
|
|
|
2886 2873 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2887 2874 <span class="s">}</span>
|
|
|
2888 2875
|
|
|
2889 2876 <span class="c"># Is it a Oxygen atom in Carboxylate group?</span>
|
|
|
2890 2877 <span class="c">#</span>
|
|
|
2891 <a name="IsCarboxylateOxygen-"></a>2878 <span class="k">sub </span><span class="m">IsCarboxylateOxygen</span> <span class="s">{</span>
|
|
|
2892 2879 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2893 2880
|
|
|
2894 2881 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylOxygen</span><span class="s">(</span><span class="q">'Carboxylate'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2895 2882 <span class="s">}</span>
|
|
|
2896 2883
|
|
|
2897 2884 <span class="c"># Is it a Carbon atom in Carboxylate group?</span>
|
|
|
2898 2885 <span class="c">#</span>
|
|
|
2899 2886 <span class="c"># Carboxyl group definition: R-C(=O)-O-</span>
|
|
|
2900 2887 <span class="c">#</span>
|
|
|
2901 <a name="IsCarboxylateCarbon-"></a>2888 <span class="k">sub </span><span class="m">IsCarboxylateCarbon</span> <span class="s">{</span>
|
|
|
2902 2889 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2903 2890
|
|
|
2904 2891 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="q">'Carboxylate'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2905 2892 <span class="s">}</span>
|
|
|
2906 2893
|
|
|
2907 2894 <span class="c"># Is it a Oxygen atom in Carboxyl group?</span>
|
|
|
2908 2895 <span class="c">#</span>
|
|
|
2909 <a name="IsCarboxylOxygen-"></a>2896 <span class="k">sub </span><span class="m">IsCarboxylOxygen</span> <span class="s">{</span>
|
|
|
2910 2897 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2911 2898
|
|
|
2912 2899 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylOxygen</span><span class="s">(</span><span class="q">'Carboxyl'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2913 2900 <span class="s">}</span>
|
|
|
2914 2901
|
|
|
2915 2902 <span class="c"># Is it a Carbon atom in Carboxyl group?</span>
|
|
|
2916 2903 <span class="c">#</span>
|
|
|
2917 2904 <span class="c"># Carboxyl group definition: R-C(=O)-OH</span>
|
|
|
2918 2905 <span class="c">#</span>
|
|
|
2919 <a name="IsCarboxylCarbon-"></a>2906 <span class="k">sub </span><span class="m">IsCarboxylCarbon</span> <span class="s">{</span>
|
|
|
2920 2907 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2921 2908
|
|
|
2922 2909 <span class="k">return</span> <span class="i">$This</span><span class="i">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="q">'Carboxyl'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2923 2910 <span class="s">}</span>
|
|
|
2924 2911
|
|
|
2925 2912 <span class="c"># Match Carboxylate and/or Carboxyl oxygen...</span>
|
|
|
2926 2913 <span class="c">#</span>
|
|
|
2927 <a name="_MatchCarboxylateAndOrCarboxylOxygen-"></a>2914 <span class="k">sub </span><span class="m">_MatchCarboxylateAndOrCarboxylOxygen</span> <span class="s">{</span>
|
|
|
2928 2915 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2929 2916
|
|
|
2930 2917 <span class="c"># Is it Oxygen?</span>
|
|
|
2931 2918 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsOxygen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2932 2919 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2933 2920 <span class="s">}</span>
|
|
|
2934 2921
|
|
|
2935 2922 <span class="c"># Is it connected to a Carboxylate Carbon?</span>
|
|
|
2936 2923 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2937 2924
|
|
|
2938 2925 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2939 2926 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2940 2927 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2941 2928 <span class="s">}</span>
|
|
|
2942 2929 <span class="s">}</span>
|
|
|
2943 2930
|
|
|
2944 2931 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2945 2932 <span class="s">}</span>
|
|
|
2946 2933
|
|
|
2947 2934 <span class="c"># Match Carboxylate and Carboxyl Carbon</span>
|
|
|
2948 2935 <span class="c">#</span>
|
|
|
2949 2936 <span class="c"># Carboxylate group definition: R-C(=O)-O-</span>
|
|
|
2950 2937 <span class="c"># Carboxyl group definition: R-C(=O)-OH</span>
|
|
|
2951 2938 <span class="c">#</span>
|
|
|
2952 2939 <span class="c"># where:</span>
|
|
|
2953 2940 <span class="c"># . R = Hydrogens or groups of atoms attached through Carbon</span>
|
|
|
2954 2941 <span class="c">#</span>
|
|
|
2955 <a name="_MatchCarboxylateAndOrCarboxylCarbon-"></a>2942 <span class="k">sub </span><span class="m">_MatchCarboxylateAndOrCarboxylCarbon</span> <span class="s">{</span>
|
|
|
2956 2943 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2957 2944
|
|
|
2958 2945 <span class="c"># Is this atom in a molecule?</span>
|
|
|
2959 2946 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2960 2947 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2961 2948 <span class="s">}</span>
|
|
|
2962 2949
|
|
|
2963 2950 <span class="c"># Is it Carbon?</span>
|
|
|
2964 2951 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2965 2952 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2966 2953 <span class="s">}</span>
|
|
|
2967 2954
|
|
|
2968 2955 <span class="c"># Match atom neighborhood...</span>
|
|
|
2969 2956 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2970 2957
|
|
|
2971 2958 <span class="i">$CentralAtomSpec</span> = <span class="q">'C.X3.BO4,C.X2.BO3'</span><span class="sc">;</span>
|
|
|
2972 2959 <span class="j">MODE:</span> <span class="s">{</span>
|
|
|
2973 2960 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Carboxylate$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2974 2961 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O.X1.FC-1'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2975 2962 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span>
|
|
|
2976 2963 <span class="s">}</span>
|
|
|
2977 2964 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Carboxyl$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2978 2965 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O.X1.FC0'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2979 2966 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span>
|
|
|
2980 2967 <span class="s">}</span>
|
|
|
2981 2968 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^CarboxylateOrCarboxyl$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2982 2969 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O.X1.FC-1,O.X1.FC0'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2983 2970 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span>
|
|
|
2984 2971 <span class="s">}</span>
|
|
|
2985 2972 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_MatchCarboxylateAndCarboxylCarbon.: Unknown mode $Mode..."</span><span class="sc">;</span>
|
|
|
2986 2973 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2987 2974 <span class="s">}</span>
|
|
|
2988 2975 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2989 2976 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C'</span><span class="cm">,</span> <span class="q">'C'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2990 2977
|
|
|
2991 2978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2992 2979 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2993 2980 <span class="s">}</span>
|
|
|
2994 2981
|
|
|
2995 2982 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2996 2983 <span class="s">}</span>
|
|
|
2997 2984
|
|
|
2998 2985 <span class="c"># Is it a Oxygen atom in Phosphate group?</span>
|
|
|
2999 2986 <span class="c">#</span>
|
|
|
3000 <a name="IsPhosphateOxygen-"></a>2987 <span class="k">sub </span><span class="m">IsPhosphateOxygen</span> <span class="s">{</span>
|
|
|
3001 2988 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3002 2989
|
|
|
3003 2990 <span class="c"># Is it Oxygen?</span>
|
|
|
3004 2991 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsOxygen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3005 2992 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3006 2993 <span class="s">}</span>
|
|
|
3007 2994
|
|
|
3008 2995 <span class="c"># Is it connected to a Phosphate Phosphorus?</span>
|
|
|
3009 2996 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3010 2997
|
|
|
3011 2998 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3012 2999 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">->IsPhosphatePhosphorus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3013 3000 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3014 3001 <span class="s">}</span>
|
|
|
3015 3002 <span class="s">}</span>
|
|
|
3016 3003
|
|
|
3017 3004 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3018 3005 <span class="s">}</span>
|
|
|
3019 3006
|
|
|
3020 3007 <span class="c"># Is it a Phosphorus atom in Phosphate group?</span>
|
|
|
3021 3008 <span class="c">#</span>
|
|
|
3022 3009 <span class="c"># Phosphate group definition: AO-(O=)P(-OA)-OA</span>
|
|
|
3023 3010 <span class="c">#</span>
|
|
|
3024 3011 <span class="c"># where:</span>
|
|
|
3025 3012 <span class="c"># . A = Any Groups of atoms including hydrogens</span>
|
|
|
3026 3013 <span class="c">#</span>
|
|
|
3027 <a name="IsPhosphatePhosphorus-"></a>3014 <span class="k">sub </span><span class="m">IsPhosphatePhosphorus</span> <span class="s">{</span>
|
|
|
3028 3015 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3029 3016
|
|
|
3030 3017 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3031 3018 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3032 3019 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3033 3020 <span class="s">}</span>
|
|
|
3034 3021
|
|
|
3035 3022 <span class="c"># Is it Phosphorus?</span>
|
|
|
3036 3023 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsPhosphorus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3037 3024 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3038 3025 <span class="s">}</span>
|
|
|
3039 3026
|
|
|
3040 3027 <span class="c"># Match atom neighborhood...</span>
|
|
|
3041 3028 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3042 3029
|
|
|
3043 3030 <span class="i">$CentralAtomSpec</span> = <span class="q">'P.X4.BO5'</span><span class="sc">;</span>
|
|
|
3044 3031 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3045 3032 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3046 3033 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3047 3034
|
|
|
3048 3035 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3049 3036 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3050 3037 <span class="s">}</span>
|
|
|
3051 3038
|
|
|
3052 3039 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3053 3040 <span class="s">}</span>
|
|
|
3054 3041
|
|
|
3055 3042
|
|
|
3056 3043 <span class="c"># Match central atom and its neighborhood using specified atom and bonds specifications...</span>
|
|
|
3057 3044 <span class="c">#</span>
|
|
|
3058 3045 <span class="c"># Let:</span>
|
|
|
3059 3046 <span class="c"># AS = Atom symbol corresponding to element symbol, atomic number (#n) or any</span>
|
|
|
3060 3047 <span class="c"># atom (A)</span>
|
|
|
3061 3048 <span class="c">#</span>
|
|
|
3062 3049 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
3063 3050 <span class="c"># T<n> = Total number of atom neighbors including implcit and explicit hydrogens</span>
|
|
|
3064 3051 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
3065 3052 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
3066 3053 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
3067 3054 <span class="c"># TSB<n> = Total number of single bonds to atom neighbors including implcit and explicit hydrogens</span>
|
|
|
3068 3055 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
3069 3056 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
3070 3057 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span>
|
|
|
3071 3058 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span>
|
|
|
3072 3059 <span class="c"># RA or RA<n> = Ring atom annotation indicating whether atom is a ring</span>
|
|
|
3073 3060 <span class="c"># TR<n> = Total number of rings containing atom</span>
|
|
|
3074 3061 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span>
|
|
|
3075 3062 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span>
|
|
|
3076 3063 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
|
|
|
3077 3064 <span class="c">#</span>
|
|
|
3078 3065 <span class="c"># Then:</span>
|
|
|
3079 3066 <span class="c">#</span>
|
|
|
3080 3067 <span class="c"># Atom specification corresponds to:</span>
|
|
|
3081 3068 <span class="c">#</span>
|
|
|
3082 3069 <span class="c"># AS.X<n>.T<n>.BO<n>.LBO<n>.<SB><n>.TSB<n>.<DB><n>.<TB><n>.H<n>.Ar.RA<n>.TR<n>FC<+n/-n>.MN<n>.SM<n></span>
|
|
|
3083 3070 <span class="c">#</span>
|
|
|
3084 3071 <span class="c"># Except for AS which is a required atomic invariant in atom specification, all other atomic invariants are</span>
|
|
|
3085 3072 <span class="c"># optional. For an atom specification to match an atom, the values of all specified atomic invariants must</span>
|
|
|
3086 3073 <span class="c"># match. Exclamation in from of atomic invariant can be used to negate its effect during the match.</span>
|
|
|
3087 3074 <span class="c">#</span>
|
|
|
3088 3075 <span class="c"># A comma delimited atom specification string is used to match any one of the specifed atom specification.</span>
|
|
|
3089 3076 <span class="c">#</span>
|
|
|
3090 3077 <span class="c"># Notes:</span>
|
|
|
3091 3078 <span class="c"># . During atom specification match to an atom, the first atomic invariant is always assumed to</span>
|
|
|
3092 3079 <span class="c"># atom symbol.</span>
|
|
|
3093 3080 <span class="c"># . Atom match specfication is based on AtomicInvariantAtomTypes implemented in</span>
|
|
|
3094 3081 <span class="c"># AotmTypes::AtomicInvariantAtomType.pm module</span>
|
|
|
3095 3082 <span class="c">#</span>
|
|
|
3096 3083 <span class="c"># Examples:</span>
|
|
|
3097 3084 <span class="c"># . ('N', 'N', 'N')</span>
|
|
|
3098 3085 <span class="c"># . ('N.FC0', 'N.FC0', 'N,N.FC+1.H1')</span>
|
|
|
3099 3086 <span class="c"># . ('N.H2', 'N.H2', 'N.H1')</span>
|
|
|
3100 3087 <span class="c"># . ('C,N', '!N', '!H')</span>
|
|
|
3101 3088 <span class="c"># . ('C,N', 'N.Ar', 'N.R5')</span>
|
|
|
3102 3089 <span class="c">#</span>
|
|
|
3103 3090 <span class="c"># Let:</span>
|
|
|
3104 3091 <span class="c"># -|1|s|Single = Single bond</span>
|
|
|
3105 3092 <span class="c"># =|2|d|Double = Double bond</span>
|
|
|
3106 3093 <span class="c"># #|3|t|Triple = Triple bond</span>
|
|
|
3107 3094 <span class="c"># :|1.5|a|Ar|Aromatic = Aromatic bond</span>
|
|
|
3108 3095 <span class="c">#</span>
|
|
|
3109 3096 <span class="c"># @|RB|Ring = Ring bond</span>
|
|
|
3110 3097 <span class="c"># ~|*|Any = Any bond</span>
|
|
|
3111 3098 <span class="c">#</span>
|
|
|
3112 3099 <span class="c"># Then:</span>
|
|
|
3113 3100 <span class="c">#</span>
|
|
|
3114 3101 <span class="c"># Bond specification corresponds to:</span>
|
|
|
3115 3102 <span class="c">#</span>
|
|
|
3116 3103 <span class="c"># -.:</span>
|
|
|
3117 3104 <span class="c"># =.@</span>
|
|
|
3118 3105 <span class="c"># Double.Aromatic</span>
|
|
|
3119 3106 <span class="c">#</span>
|
|
|
3120 3107 <span class="c"># For a bond specification to match bond between two atoms, the values of all specified bond symbols must</span>
|
|
|
3121 3108 <span class="c"># match. Exclamation in from of bond symbol can be used to negate its effect during the match.</span>
|
|
|
3122 3109 <span class="c">#</span>
|
|
|
3123 3110 <span class="c"># A comma delimited bond specification string is used to match any one of the specifed atom specification.</span>
|
|
|
3124 3111 <span class="c">#</span>
|
|
|
3125 <a name="DoesAtomNeighborhoodMatch-"></a>3112 <span class="k">sub </span><span class="m">DoesAtomNeighborhoodMatch</span> <span class="s">{</span>
|
|
|
3126 3113 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="cm">,</span> <span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3127 3114 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NumOfNbrBondSpecs</span><span class="cm">,</span> <span class="i">$NumOfNbrOfNbrAtomSpecs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3128 3115
|
|
|
3129 3116 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3130 3117 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CentralAtom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3131 3118 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3132 3119 <span class="s">}</span>
|
|
|
3133 3120
|
|
|
3134 3121 <span class="i">$NumOfNbrAtomSpecs</span> = <span class="k">defined</span> <span class="i">$NbrAtomSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrAtomSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3135 3122 <span class="i">$NumOfNbrBondSpecs</span> = <span class="k">defined</span> <span class="i">$NbrBondSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrBondSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3136 3123 <span class="i">$NumOfNbrOfNbrAtomSpecs</span> = <span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrOfNbrAtomSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3137 3124
|
|
|
3138 3125 <span class="c"># Validate number of specifications...</span>
|
|
|
3139 3126 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrBondSpecs</span> && <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> != <span class="i">$NumOfNbrBondSpecs</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3140 3127 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DoesAtomNeighborhoodMatch: Number of specified central atom, $NumOfNbrAtomSpecs, and bond, $NumOfNbrBondSpecs, specifications must be same; No neighborhood match performed ..."</span><span class="sc">;</span>
|
|
|
3141 3128 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3142 3129 <span class="s">}</span>
|
|
|
3143 3130
|
|
|
3144 3131 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrOfNbrAtomSpecs</span> && <span class="s">(</span><span class="i">$NumOfNbrOfNbrAtomSpecs</span> != <span class="i">$NumOfNbrAtomSpecs</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3145 3132 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DoesAtomNeighborhoodMatch: Number of specified central atom, $NumOfNbrAtomSpecs, and neighbor of neighbor atoms specifications, $NumOfNbrOfNbrAtomSpecs, must be same; No neighborhood match performed ..."</span><span class="sc">;</span>
|
|
|
3146 3133 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3147 3134 <span class="s">}</span>
|
|
|
3148 3135
|
|
|
3149 3136 <span class="c"># Sort atom and bond specifications in terms of being most specific to least specific..</span>
|
|
|
3150 3137 <span class="s">(</span><span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">$CentralAtom</span><span class="i">->_SortSpecificationsForAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3151 3138
|
|
|
3152 3139 <span class="c"># Does central atom specification match?</span>
|
|
|
3153 3140 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CentralAtom</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3154 3141 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3155 3142 <span class="s">}</span>
|
|
|
3156 3143
|
|
|
3157 3144 <span class="c"># No neighbors to match...</span>
|
|
|
3158 3145 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfNbrAtomSpecs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3159 3146 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3160 3147 <span class="s">}</span>
|
|
|
3161 3148
|
|
|
3162 3149 <span class="c"># Match neighbors...</span>
|
|
|
3163 3150 <span class="k">my</span><span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> <span class="i">%NbrSpecAlreadyMatchedMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3164 3151
|
|
|
3165 3152 <span class="i">$NbrSpecCount</span> = <span class="i">$NumOfNbrAtomSpecs</span><span class="sc">;</span>
|
|
|
3166 3153 <span class="i">$NbrSpecMatchCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3167 3154
|
|
|
3168 3155 <span class="i">%NbrSpecAlreadyMatchedMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3169 3156 <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span> = <span class="i">$CentralAtom</span><span class="i">->_MatchAtomNeighborhoodUsingAtomBondSpecs</span><span class="s">(</span><span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> \<span class="i">%NbrSpecAlreadyMatchedMap</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3170 3157
|
|
|
3171 3158 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3172 3159 <span class="c"># It's match...</span>
|
|
|
3173 3160 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3174 3161 <span class="s">}</span>
|
|
|
3175 3162
|
|
|
3176 3163 <span class="c"># Match central atom's missing hydrogens with any unmatched atom</span>
|
|
|
3177 3164 <span class="c"># and bond specifications...</span>
|
|
|
3178 3165 <span class="c">#</span>
|
|
|
3179 3166 <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span> = <span class="i">$CentralAtom</span><span class="i">->_MatchAtomNeighborhoodUsingMissingHydrogens</span><span class="s">(</span><span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> \<span class="i">%NbrSpecAlreadyMatchedMap</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3180 3167
|
|
|
3181 3168 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3182 3169 <span class="c"># It's match...</span>
|
|
|
3183 3170 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3184 3171 <span class="s">}</span>
|
|
|
3185 3172
|
|
|
3186 3173 <span class="c"># No match...</span>
|
|
|
3187 3174 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3188 3175 <span class="s">}</span>
|
|
|
3189 3176
|
|
|
3190 3177 <span class="c"># Match central atom neighborhood atom and bond specifications...</span>
|
|
|
3191 3178 <span class="c">#</span>
|
|
|
3192 <a name="_MatchAtomNeighborhoodUsingAtomBondSpecs-"></a>3179 <span class="k">sub </span><span class="m">_MatchAtomNeighborhoodUsingAtomBondSpecs</span> <span class="s">{</span>
|
|
|
3193 3180 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="cm">,</span> <span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> <span class="i">$NbrSpecAlreadyMatchedRef</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3194 3181 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$NbrAtom</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="cm">,</span> <span class="i">$NbrBondSpec</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtom</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpec</span><span class="cm">,</span> <span class="i">$MatchNbrOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrSpecsMatched</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3195 3182
|
|
|
3196 3183 <span class="i">$MatchNbrOfNbrAtomSpecs</span> = <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span> && <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrOfNbrAtomSpecsRef</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3197 3184
|
|
|
3198 3185 <span class="i">$NbrSpecsMatched</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3199 3186
|
|
|
3200 3187 <span class="c"># Match central atom's immediate neighbors atom and bond specifications...</span>
|
|
|
3201 3188 <span class="j">NBRATOM:</span> <span class="k">for</span> <span class="i">$NbrAtom</span> <span class="s">(</span><span class="i">$CentralAtom</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3202 3189 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NbrSpecCount</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3203 3190 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
3204 3191 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
|
|
|
3205 3192 <span class="s">}</span>
|
|
|
3206 3193 <span class="i">$NbrAtomSpec</span> = <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
3207 3194 <span class="i">$NbrBondSpec</span> = <span class="i">$NbrBondSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
3208 3195
|
|
|
3209 3196 <span class="i">$NbrOfNbrAtomSpec</span> = <span class="i">$MatchNbrOfNbrAtomSpecs</span> ? <span class="i">$NbrOfNbrAtomSpecsRef</span>->[<span class="i">$Index</span>] <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3210 3197
|
|
|
3211 3198 <span class="c"># Match neighbor atom specification...</span>
|
|
|
3212 3199 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NbrAtom</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$NbrAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3213 3200 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
|
|
|
3214 3201 <span class="s">}</span>
|
|
|
3215 3202
|
|
|
3216 3203 <span class="c"># Match central atom to neighbor atom bond specification...</span>
|
|
|
3217 3204 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CentralAtom</span><span class="i">->_DoesBondSpecificationMatch</span><span class="s">(</span><span class="i">$NbrAtom</span><span class="cm">,</span> <span class="i">$NbrBondSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3218 3205 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
|
|
|
3219 3206 <span class="s">}</span>
|
|
|
3220 3207
|
|
|
3221 3208 <span class="c"># Match any neighbor of neighbor atom specifications...</span>
|
|
|
3222 3209 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3223 3210 <span class="c"># Go over the neighbors of central atom skipping the central atom...</span>
|
|
|
3224 3211 <span class="k">for</span> <span class="i">$NbrOfNbrAtom</span> <span class="s">(</span><span class="i">$NbrAtom</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3225 3212 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NbrOfNbrAtom</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$NbrOfNbrAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3226 3213 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
|
|
|
3227 3214 <span class="s">}</span>
|
|
|
3228 3215 <span class="s">}</span>
|
|
|
3229 3216 <span class="s">}</span>
|
|
|
3230 3217
|
|
|
3231 3218 <span class="c"># It's a match for a neighbor atom specification...</span>
|
|
|
3232 3219 <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>} = <span class="i">$Index</span><span class="sc">;</span>
|
|
|
3233 3220 <span class="i">$NbrSpecMatchCount</span>++<span class="sc">;</span>
|
|
|
3234 3221
|
|
|
3235 3222 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecMatchCount</span> == <span class="i">$NbrSpecCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3236 3223 <span class="c"># It's match...</span>
|
|
|
3237 3224 <span class="i">$NbrSpecsMatched</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3238 3225 <span class="k">last</span> <span class="j">NBRATOM</span><span class="sc">;</span>
|
|
|
3239 3226 <span class="s">}</span>
|
|
|
3240 3227 <span class="c"># Match next neighbor atom...</span>
|
|
|
3241 3228 <span class="k">next</span> <span class="j">NBRATOM</span><span class="sc">;</span>
|
|
|
3242 3229 <span class="s">}</span>
|
|
|
3243 3230 <span class="s">}</span>
|
|
|
3244 3231 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3245 3232 <span class="s">}</span>
|
|
|
3246 3233
|
|
|
3247 3234 <span class="c"># Match central atom's missing hydrogens with any unmatched atom and bond</span>
|
|
|
3248 3235 <span class="c"># specifications...</span>
|
|
|
3249 3236 <span class="c">#</span>
|
|
|
3250 <a name="_MatchAtomNeighborhoodUsingMissingHydrogens-"></a>3237 <span class="k">sub </span><span class="m">_MatchAtomNeighborhoodUsingMissingHydrogens</span> <span class="s">{</span>
|
|
|
3251 3238 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="cm">,</span> <span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> <span class="i">$NbrSpecAlreadyMatchedRef</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3252 3239 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$NbrAtom</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="cm">,</span> <span class="i">$NbrBondSpec</span><span class="cm">,</span> <span class="i">$NumOfMissingHydrogens</span><span class="cm">,</span> <span class="i">$MissingHydrogensIndex</span><span class="cm">,</span> <span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$AtomSpecMatched</span><span class="cm">,</span> <span class="i">$AtomSpec</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3253 3240
|
|
|
3254 3241 <span class="i">$NbrSpecsMatched</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3255 3242
|
|
|
3256 3243 <span class="i">$NumOfMissingHydrogens</span> = <span class="i">$CentralAtom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3257 3244 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$NbrSpecCount</span> - <span class="i">$NbrSpecMatchCount</span><span class="s">)</span> > <span class="i">$NumOfMissingHydrogens</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3258 3245 <span class="c"># It won't match...</span>
|
|
|
3259 3246 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3260 3247 <span class="s">}</span>
|
|
|
3261 3248
|
|
|
3262 3249 <span class="j">MISSINGHYDROGENNBR:</span> <span class="k">for</span> <span class="i">$MissingHydrogensIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfMissingHydrogens</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3263 3250 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NbrSpecCount</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3264 3251 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
3265 3252 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
|
|
|
3266 3253 <span class="s">}</span>
|
|
|
3267 3254 <span class="i">$NbrAtomSpec</span> = <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
3268 3255 <span class="i">$NbrBondSpec</span> = <span class="i">$NbrBondSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
3269 3256
|
|
|
3270 3257 <span class="i">$NbrAtomSpec</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
3271 3258
|
|
|
3272 3259 <span class="c"># Match neighbor atom specification hydrogen atom symbol...</span>
|
|
|
3273 3260 <span class="i">$AtomSpecMatched</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3274 3261 <span class="j">ATOMSPEC:</span> <span class="k">for</span> <span class="i">$AtomSpec</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3275 3262 <span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AtomSpec</span><span class="sc">;</span>
|
|
|
3276 3263 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomSymbol</span> =~ <span class="q">/^(H|A|\*)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3277 3264 <span class="i">$AtomSpecMatched</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3278 3265 <span class="k">last</span> <span class="j">ATOMSPEC</span><span class="sc">;</span>
|
|
|
3279 3266 <span class="s">}</span>
|
|
|
3280 3267 <span class="s">}</span>
|
|
|
3281 3268 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSpecMatched</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3282 3269 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
|
|
|
3283 3270 <span class="s">}</span>
|
|
|
3284 3271
|
|
|
3285 3272 <span class="c"># Match neighbor atom bond specification to singal bond...</span>
|
|
|
3286 3273 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrBondSpec</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3287 3274 <span class="i">$NbrBondSpec</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
3288 3275 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrBondSpec</span> !~ <span class="q">/^(-|1|s|Single|\~|\*|Any)/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3289 3276 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
|
|
|
3290 3277 <span class="s">}</span>
|
|
|
3291 3278 <span class="s">}</span>
|
|
|
3292 3279
|
|
|
3293 3280 <span class="c"># It's a match for a neighbor atom specification...</span>
|
|
|
3294 3281 <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$Index</span>} = <span class="i">$Index</span><span class="sc">;</span>
|
|
|
3295 3282 <span class="i">$NbrSpecMatchCount</span>++<span class="sc">;</span>
|
|
|
3296 3283
|
|
|
3297 3284 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecMatchCount</span> == <span class="i">$NbrSpecCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3298 3285 <span class="c"># It's match...</span>
|
|
|
3299 3286 <span class="i">$NbrSpecsMatched</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3300 3287 <span class="k">last</span> <span class="j">MISSINGHYDROGENNBR</span><span class="sc">;</span>
|
|
|
3301 3288 <span class="s">}</span>
|
|
|
3302 3289 <span class="c"># Match next missing hydrogen neighbor...</span>
|
|
|
3303 3290 <span class="k">next</span> <span class="j">MISSINGHYDROGENNBR</span><span class="sc">;</span>
|
|
|
3304 3291 <span class="s">}</span>
|
|
|
3305 3292 <span class="s">}</span>
|
|
|
3306 3293
|
|
|
3307 3294 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3308 3295 <span class="s">}</span>
|
|
|
3309 3296
|
|
|
3310 3297 <span class="c"># Sort atom and bond specifications base on neighbor atom specifications going</span>
|
|
|
3311 3298 <span class="c"># from most to least specific atom specifications.</span>
|
|
|
3312 3299 <span class="c">#</span>
|
|
|
3313 3300 <span class="c"># Atom specifications are sorted at the following two levels:</span>
|
|
|
3314 3301 <span class="c">#</span>
|
|
|
3315 3302 <span class="c"># o By atom specification count with in each specification going from most specific</span>
|
|
|
3316 3303 <span class="c"># to least specific, where count is determined by the number of "," in each</span>
|
|
|
3317 3304 <span class="c"># specification. Wild card containing specifications are considered least specific</span>
|
|
|
3318 3305 <span class="c"># and end up at the end of the sorted list.</span>
|
|
|
3319 3306 <span class="c"># o By atomic invariant count with in each sorted list going from most specific to</span>
|
|
|
3320 3307 <span class="c"># least specific, where count is determined by the number of "." in each atom</span>
|
|
|
3321 3308 <span class="c"># specification.</span>
|
|
|
3322 3309 <span class="c">#</span>
|
|
|
3323 3310 <span class="c">#A single atom specification,</span>
|
|
|
3324 3311 <span class="c"># without any commas in atom specification, is is considered most specific...</span>
|
|
|
3325 3312 <span class="c">#</span>
|
|
|
3326 <a name="_SortSpecificationsForAtomNeighborhoodMatch-"></a>3313 <span class="k">sub </span><span class="m">_SortSpecificationsForAtomNeighborhoodMatch</span> <span class="s">{</span>
|
|
|
3327 3314 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3328 3315 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$NeedToSort</span><span class="cm">,</span> <span class="i">$NumOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrAtomSpecCount</span><span class="cm">,</span> <span class="i">$NbrAtomSpecAtomicInvarintCount</span><span class="cm">,</span> <span class="i">$NbrAtomSpecToMatch</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="cm">,</span> <span class="i">$FirstAtomicInvariant</span><span class="cm">,</span> <span class="i">$WildCardInNbrAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecs</span><span class="cm">,</span> <span class="i">@NbrAtomSpecAtomicInvariants</span><span class="cm">,</span> <span class="i">@SortedNbrAtomSpecs</span><span class="cm">,</span> <span class="i">@SortedNbrBondSpecs</span><span class="cm">,</span> <span class="i">@SortedNbrOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">%NbrAtomSpecDataMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3329 3316
|
|
|
3330 3317 <span class="i">$NumOfNbrAtomSpecs</span> = <span class="k">defined</span> <span class="i">$NbrAtomSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrAtomSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3331 3318
|
|
|
3332 3319 <span class="c"># Figure out whether sorting is necessary...</span>
|
|
|
3333 3320 <span class="i">$NeedToSort</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3334 3321 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3335 3322 <span class="j">ATOMSPEC:</span> <span class="k">for</span> <span class="i">$NbrAtomSpecToMatch</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NbrAtomSpecsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
3336 3323 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">/(,|\.|A|\*)/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3337 3324 <span class="i">$NeedToSort</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3338 3325 <span class="k">last</span> <span class="j">ATOMSPEC</span><span class="sc">;</span>
|
|
|
3339 3326 <span class="s">}</span>
|
|
|
3340 3327 <span class="s">}</span>
|
|
|
3341 3328 <span class="s">}</span>
|
|
|
3342 3329 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NeedToSort</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3343 3330 <span class="c"># Nothing to do...</span>
|
|
|
3344 3331 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3345 3332 <span class="s">}</span>
|
|
|
3346 3333
|
|
|
3347 3334 <span class="i">%NbrAtomSpecDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3348 3335
|
|
|
3349 3336 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3350 3337 <span class="i">$NbrAtomSpecToMatch</span> = <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
3351 3338 <span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
3352 3339
|
|
|
3353 3340 <span class="i">@NbrAtomSpecs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NbrAtomSpecToMatch</span><span class="sc">;</span>
|
|
|
3354 3341 <span class="i">$NbrAtomSpecCount</span> = <span class="k">scalar</span> <span class="i">@NbrAtomSpecs</span><span class="sc">;</span>
|
|
|
3355 3342
|
|
|
3356 3343 <span class="c"># Does neighbor specification contains a wild card in atom symbol specification?</span>
|
|
|
3357 3344 <span class="c">#</span>
|
|
|
3358 3345 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">/(A|\*)/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3359 3346 <span class="i">$WildCardInNbrAtomSpec</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3360 3347 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$NbrAtomSpec</span> <span class="s">(</span><span class="i">@NbrAtomSpecs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3361 3348 <span class="s">(</span><span class="i">$FirstAtomicInvariant</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="sc">;</span>
|
|
|
3362 3349 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3363 3350 <span class="i">$FirstAtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span>
|
|
|
3364 3351 <span class="s">}</span>
|
|
|
3365 3352 <span class="i">$WildCardInNbrAtomSpec</span> = <span class="i">$This</span><span class="i">->_IsWildCardAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$FirstAtomicInvariant</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3366 3353 <span class="k">if</span> <span class="s">(</span><span class="i">$WildCardInNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3367 3354 <span class="k">last</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
|
|
|
3368 3355 <span class="s">}</span>
|
|
|
3369 3356 <span class="s">}</span>
|
|
|
3370 3357 <span class="k">if</span> <span class="s">(</span><span class="i">$WildCardInNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3371 3358 <span class="c"># Set NbrAtomSpecCount arbitrarily high to make the spec containing wild</span>
|
|
|
3372 3359 <span class="c"># card last on the sorted list while maintaining its original order in the list...</span>
|
|
|
3373 3360 <span class="i">$NbrAtomSpecCount</span> = <span class="n">999</span><span class="sc">;</span>
|
|
|
3374 3361 <span class="s">}</span>
|
|
|
3375 3362 <span class="s">}</span>
|
|
|
3376 3363
|
|
|
3377 3364 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
3378 3365 <span class="i">%</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3379 3366 <span class="s">}</span>
|
|
|
3380 3367
|
|
|
3381 3368 <span class="c"># Use first NbrAtomSpec available in @NbrAtomSpecs to determine atomic invariant count</span>
|
|
|
3382 3369 <span class="c"># with in each NbrAtomSpecToMatch, as @NbrAtomSpecs derived from $NbrAtomSpecToMatch</span>
|
|
|
3383 3370 <span class="c"># simply corresponds to a list of possible matches...</span>
|
|
|
3384 3371 <span class="c">#</span>
|
|
|
3385 3372 <span class="s">(</span><span class="i">$NbrAtomSpec</span><span class="s">)</span> = <span class="i">@NbrAtomSpecs</span><span class="sc">;</span>
|
|
|
3386 3373 <span class="i">@NbrAtomSpecAtomicInvariants</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="sc">;</span>
|
|
|
3387 3374 <span class="i">$NbrAtomSpecAtomicInvarintCount</span> = <span class="k">scalar</span> <span class="i">@NbrAtomSpecAtomicInvariants</span><span class="sc">;</span>
|
|
|
3388 3375
|
|
|
3389 3376 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
3390 3377 <span class="i">@</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3391 3378 <span class="s">}</span>
|
|
|
3392 3379 <span class="k">push</span> <span class="i">@</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}}<span class="cm">,</span> <span class="i">$Index</span><span class="sc">;</span>
|
|
|
3393 3380
|
|
|
3394 3381 <span class="s">}</span>
|
|
|
3395 3382
|
|
|
3396 3383 <span class="i">@SortedNbrAtomSpecs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@SortedNbrBondSpecs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3397 3384 <span class="i">@SortedNbrOfNbrAtomSpecs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3398 3385
|
|
|
3399 3386 <span class="k">for</span> <span class="i">$NbrAtomSpecCount</span> <span class="s">(</span> <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%NbrAtomSpecDataMap</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3400 3387 <span class="k">for</span> <span class="i">$NbrAtomSpecAtomicInvarintCount</span> <span class="s">(</span> <span class="k">sort</span> <span class="s">{</span> <span class="i">$b</span> <=> <span class="i">$a</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
3401 3388 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
3402 3389 <span class="k">push</span> <span class="i">@SortedNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
3403 3390 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrBondSpecsRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3404 3391 <span class="k">push</span> <span class="i">@SortedNbrBondSpecs</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
3405 3392 <span class="s">}</span>
|
|
|
3406 3393 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3407 3394 <span class="k">push</span> <span class="i">@SortedNbrOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
3408 3395 <span class="s">}</span>
|
|
|
3409 3396 <span class="s">}</span>
|
|
|
3410 3397 <span class="s">}</span>
|
|
|
3411 3398 <span class="s">}</span>
|
|
|
3412 3399
|
|
|
3413 3400 <span class="k">return</span> <span class="s">(</span>\<span class="i">@SortedNbrAtomSpecs</span><span class="cm">,</span> <span class="k">defined</span> <span class="i">$NbrBondSpecsRef</span> ? \<span class="i">@SortedNbrBondSpecs</span> <span class="co">:</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span> ? \<span class="i">@SortedNbrOfNbrAtomSpecs</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3414 3401 <span class="s">}</span>
|
|
|
3415 3402
|
|
|
3416 3403 <span class="c"># Check whether atom matches supported atom specification...</span>
|
|
|
3417 3404 <span class="c">#</span>
|
|
|
3418 <a name="_DoesAtomSpecificationMatch-"></a>3405 <span class="k">sub </span><span class="m">_DoesAtomSpecificationMatch</span> <span class="s">{</span>
|
|
|
3419 3406 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomSpecificationToMatch</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3420 3407 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomSpecificationMatched</span><span class="cm">,</span> <span class="i">$AtomicInvariantMatched</span><span class="cm">,</span> <span class="i">$FirstMatch</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3421 3408
|
|
|
3422 3409 <span class="c"># Anything to match...</span>
|
|
|
3423 3410 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$AtomSpecificationToMatch</span><span class="s">)</span> && <span class="i">$AtomSpecificationToMatch</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3424 3411 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3425 3412 <span class="s">}</span>
|
|
|
3426 3413
|
|
|
3427 3414 <span class="c"># Take out any spaces...</span>
|
|
|
3428 3415 <span class="i">$AtomSpecificationToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
3429 3416
|
|
|
3430 3417 <span class="c"># Match specified atom specifications. For multiple atom specifications in a comma delimited string,</span>
|
|
|
3431 3418 <span class="c"># only one atom specification needs to match for a successful match. It's up to the caller to make</span>
|
|
|
3432 3419 <span class="c"># sure that the specificaton list is ordered from least to most specific atom specification...</span>
|
|
|
3433 3420 <span class="c">#</span>
|
|
|
3434 3421 <span class="k">for</span> <span class="i">$AtomSpecification</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$AtomSpecificationToMatch</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3435 3422 <span class="i">$AtomSpecificationMatched</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3436 3423 <span class="i">$FirstMatch</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3437 3424
|
|
|
3438 3425 <span class="c"># Match all atom symbol atomic invariants...</span>
|
|
|
3439 3426 <span class="j">ATOMICINVARIANT:</span> <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AtomSpecification</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3440 3427 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstMatch</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3441 3428 <span class="c"># Match atom symbol atomic invariant...</span>
|
|
|
3442 3429 <span class="i">$FirstMatch</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3443 3430 <span class="i">$AtomicInvariantMatched</span> = <span class="i">$This</span><span class="i">->_MatchAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3444 3431 <span class="s">}</span>
|
|
|
3445 3432 <span class="k">else</span> <span class="s">{</span>
|
|
|
3446 3433 <span class="c"># Match non atom symbol atomic invariant...</span>
|
|
|
3447 3434 <span class="i">$AtomicInvariantMatched</span> = <span class="i">$This</span><span class="i">->_MatchNonAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3448 3435 <span class="s">}</span>
|
|
|
3449 3436
|
|
|
3450 3437 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicInvariantMatched</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3451 3438 <span class="c"># No need to match other atomic invariants...</span>
|
|
|
3452 3439 <span class="i">$AtomSpecificationMatched</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3453 3440 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span>
|
|
|
3454 3441 <span class="s">}</span>
|
|
|
3455 3442 <span class="s">}</span>
|
|
|
3456 3443
|
|
|
3457 3444 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomSpecificationMatched</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3458 3445 <span class="c"># No need to match other atom specifications...</span>
|
|
|
3459 3446 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3460 3447 <span class="s">}</span>
|
|
|
3461 3448 <span class="s">}</span>
|
|
|
3462 3449
|
|
|
3463 3450 <span class="c"># Nothing matched...</span>
|
|
|
3464 3451 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3465 3452 <span class="s">}</span>
|
|
|
3466 3453
|
|
|
3467 3454 <span class="c"># Check whether atom matches atom symbol atomic invariant...</span>
|
|
|
3468 3455 <span class="c">#</span>
|
|
|
3469 <a name="_MatchAtomSymbolAtomicInvariant-"></a>3456 <span class="k">sub </span><span class="m">_MatchAtomSymbolAtomicInvariant</span> <span class="s">{</span>
|
|
|
3470 3457 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3471 3458 <span class="k">my</span><span class="s">(</span><span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3472 3459
|
|
|
3473 3460 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3474 3461 <span class="i">$NegateMatch</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3475 3462
|
|
|
3476 3463 <span class="c"># Does match needs to be negated?</span>
|
|
|
3477 3464 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3478 3465 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3479 3466 <span class="i">$AtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span>
|
|
|
3480 3467 <span class="s">}</span>
|
|
|
3481 3468
|
|
|
3482 3469 <span class="j">ATOMICINVARIANT:</span> <span class="s">{</span>
|
|
|
3483 3470 <span class="c"># Any atom match...</span>
|
|
|
3484 3471 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_IsWildCardAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3485 3472 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3486 3473 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span>
|
|
|
3487 3474 <span class="s">}</span>
|
|
|
3488 3475
|
|
|
3489 3476 <span class="c"># Atomic number match...</span>
|
|
|
3490 3477 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3491 3478 <span class="i">$AtomicNumber</span> = <span class="i">$AtomicInvariant</span><span class="sc">;</span> <span class="i">$AtomicNumber</span> =~ <span class="q">s/^#//</span><span class="sc">;</span>
|
|
|
3492 3479 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="i">$AtomicNumber</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3493 3480 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span>
|
|
|
3494 3481 <span class="s">}</span>
|
|
|
3495 3482
|
|
|
3496 3483 <span class="c"># Atom symbol match...</span>
|
|
|
3497 3484 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomSymbol</span>} =~ <span class="q">/^$AtomicInvariant$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3498 3485 <span class="s">}</span>
|
|
|
3499 3486
|
|
|
3500 3487 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3501 3488 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3502 3489 <span class="s">}</span>
|
|
|
3503 3490
|
|
|
3504 3491 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
3505 3492 <span class="s">}</span>
|
|
|
3506 3493
|
|
|
3507 3494 <span class="c"># Is it a wild card atom symbol atomic invariant?</span>
|
|
|
3508 3495 <span class="c">#</span>
|
|
|
3509 <a name="_IsWildCardAtomSymbolAtomicInvariant-"></a>3496 <span class="k">sub </span><span class="m">_IsWildCardAtomSymbolAtomicInvariant</span> <span class="s">{</span>
|
|
|
3510 3497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3511 3498
|
|
|
3512 3499 <span class="k">return</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(A|\*)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3513 3500 <span class="s">}</span>
|
|
|
3514 3501
|
|
|
3515 3502 <span class="c"># Check whether atom matches non atom symbol atomic invariants...</span>
|
|
|
3516 3503 <span class="c">#</span>
|
|
|
3517 <a name="_MatchNonAtomSymbolAtomicInvariant-"></a>3504 <span class="k">sub </span><span class="m">_MatchNonAtomSymbolAtomicInvariant</span> <span class="s">{</span>
|
|
|
3518 3505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3519 3506 <span class="k">my</span><span class="s">(</span><span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$UnknownName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3520 3507
|
|
|
3521 3508 <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$UnknownName</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
|
|
|
3522 3509
|
|
|
3523 3510 <span class="c"># Does match needs to be negated?</span>
|
|
|
3524 3511 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3525 3512 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3526 3513 <span class="i">$AtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span>
|
|
|
3527 3514 <span class="s">}</span>
|
|
|
3528 3515
|
|
|
3529 3516 <span class="c"># Extract atomic invariant name and any value...</span>
|
|
|
3530 3517 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/[0-9\*]+/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3531 3518 <span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">$AtomicInvariant</span> =~ <span class="q">/^([a-zA-Z]+)([0-9\-\+\*\>\<\=]+)$/</span><span class="sc">;</span>
|
|
|
3532 3519 <span class="s">}</span>
|
|
|
3533 3520 <span class="k">else</span> <span class="s">{</span>
|
|
|
3534 3521 <span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3535 3522 <span class="s">}</span>
|
|
|
3536 3523
|
|
|
3537 3524 <span class="j">NAME:</span> <span class="s">{</span>
|
|
|
3538 3525 <span class="c"># Match number of non-hydrogen atom neighbors</span>
|
|
|
3539 3526 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^X$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3540 3527 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3541 3528 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3542 3529 <span class="s">}</span>
|
|
|
3543 3530
|
|
|
3544 3531 <span class="c"># Match total number of atom neighbors including missing hydrogens...</span>
|
|
|
3545 3532 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^T$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3546 3533 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3547 3534 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3548 3535 <span class="s">}</span>
|
|
|
3549 3536
|
|
|
3550 3537 <span class="c"># Match formal charge...</span>
|
|
|
3551 3538 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^FC$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3552 3539 <span class="k">my</span> <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3553 3540 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_MatchNonAtomSymbolAtomicInvariantValue</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3554 3541 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3555 3542 <span class="s">}</span>
|
|
|
3556 3543
|
|
|
3557 3544 <span class="c"># Match aromatic annotation indicating whether atom is aromatic...</span>
|
|
|
3558 3545 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^Ar$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3559 3546 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3560 3547 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3561 3548 <span class="s">}</span>
|
|
|
3562 3549
|
|
|
3563 3550 <span class="c"># Match number of implicit and explicit hydrogens...</span>
|
|
|
3564 3551 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^H$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3565 3552 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3566 3553 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3567 3554 <span class="s">}</span>
|
|
|
3568 3555
|
|
|
3569 3556 <span class="c"># Match ring atom annotation indicating whether atom is in ring...</span>
|
|
|
3570 3557 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^RA$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3571 3558 <span class="i">$Status</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> ? <span class="i">$This</span><span class="i">->IsInRingOfSize</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3572 3559 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3573 3560 <span class="s">}</span>
|
|
|
3574 3561
|
|
|
3575 3562 <span class="c"># Match number of rings for atom..</span>
|
|
|
3576 3563 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^TR$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3577 3564 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Value</span> == <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3578 3565 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3579 3566 <span class="s">}</span>
|
|
|
3580 3567
|
|
|
3581 3568 <span class="c"># Match sum of bond orders to non-hydrogen atom neighbors...</span>
|
|
|
3582 3569 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^BO$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3583 3570 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3584 3571 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3585 3572 <span class="s">}</span>
|
|
|
3586 3573
|
|
|
3587 3574 <span class="c"># Match largest bond order of non-hydrogen atom neighbors...</span>
|
|
|
3588 3575 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^LBO$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3589 3576 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3590 3577 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3591 3578 <span class="s">}</span>
|
|
|
3592 3579
|
|
|
3593 3580 <span class="c"># Match number of single bonds to non-hydrogen atom neighbors...</span>
|
|
|
3594 3581 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^SB$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3595 3582 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3596 3583 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3597 3584 <span class="s">}</span>
|
|
|
3598 3585
|
|
|
3599 3586 <span class="c"># Match total number of single bonds to atom neighbors including missing and explicit hydrogens...</span>
|
|
|
3600 3587 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^TSB$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3601 3588 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3602 3589 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3603 3590 <span class="s">}</span>
|
|
|
3604 3591
|
|
|
3605 3592 <span class="c"># Match number of double bonds to non-hydrogen atom neighbors...</span>
|
|
|
3606 3593 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^DB$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3607 3594 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3608 3595 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3609 3596 <span class="s">}</span>
|
|
|
3610 3597
|
|
|
3611 3598 <span class="c"># Match number of triple bonds to non-hydrogen atom neighbors...</span>
|
|
|
3612 3599 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^TB$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3613 3600 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetNumOfTripleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3614 3601 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3615 3602 <span class="s">}</span>
|
|
|
3616 3603
|
|
|
3617 3604 <span class="c"># Match number of aromatic bonds to non-hydrogen atom neighbors...</span>
|
|
|
3618 3605 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^AB$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3619 3606 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3620 3607 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3621 3608 <span class="s">}</span>
|
|
|
3622 3609
|
|
|
3623 3610
|
|
|
3624 3611 <span class="c"># Match mass number indicating isotope other than most abundant isotope...</span>
|
|
|
3625 3612 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^MN$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3626 3613 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3627 3614 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3628 3615 <span class="s">}</span>
|
|
|
3629 3616
|
|
|
3630 3617 <span class="c"># Match spin multiplicity...</span>
|
|
|
3631 3618 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^SM$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3632 3619 <span class="k">my</span> <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3633 3620 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SpinMultiplicity</span><span class="s">)</span> <span class="s">{</span> <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
3634 3621 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span> && <span class="i">$Value</span> == <span class="i">$SpinMultiplicity</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3635 3622 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
3636 3623 <span class="s">}</span>
|
|
|
3637 3624
|
|
|
3638 3625 <span class="i">$UnknownName</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3639 3626 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_MatchNonAtomSymbolAtomicInvariant: Unknown atomic invariant $AtomicInvariant..."</span><span class="sc">;</span>
|
|
|
3640 3627 <span class="s">}</span>
|
|
|
3641 3628
|
|
|
3642 3629 <span class="k">if</span> <span class="s">(</span>!<span class="i">$UnknownName</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3643 3630 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3644 3631 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3645 3632 <span class="s">}</span>
|
|
|
3646 3633 <span class="s">}</span>
|
|
|
3647 3634
|
|
|
3648 3635 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
3649 3636 <span class="s">}</span>
|
|
|
3650 3637
|
|
|
3651 3638 <span class="c"># Match atomic invariant value...</span>
|
|
|
3652 3639 <span class="c">#</span>
|
|
|
3653 3640 <span class="c"># Specified value format:</span>
|
|
|
3654 3641 <span class="c"># . +* : Any positive value</span>
|
|
|
3655 3642 <span class="c"># . -* : Any negative value</span>
|
|
|
3656 3643 <span class="c"># . >ValidNumber or >=ValidNumber</span>
|
|
|
3657 3644 <span class="c"># . <ValidNumber or <=ValidNumber</span>
|
|
|
3658 3645 <span class="c"># . Any valid number</span>
|
|
|
3659 3646 <span class="c">#</span>
|
|
|
3660 <a name="_MatchNonAtomSymbolAtomicInvariantValue-"></a>3647 <span class="k">sub </span><span class="m">_MatchNonAtomSymbolAtomicInvariantValue</span> <span class="s">{</span>
|
|
|
3661 3648 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$TargetValue</span><span class="cm">,</span> <span class="i">$SpecifiedValue</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3662 3649 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3663 3650
|
|
|
3664 3651 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3665 3652
|
|
|
3666 3653 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$TargetValue</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$SpecifiedValue</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3667 3654 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
3668 3655 <span class="s">}</span>
|
|
|
3669 3656
|
|
|
3670 3657 <span class="j">VALUE:</span> <span class="s">{</span>
|
|
|
3671 3658 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^\+\*/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3672 3659 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$TargetValue</span> > <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3673 3660 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
|
|
|
3674 3661 <span class="s">}</span>
|
|
|
3675 3662 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^\-\*/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3676 3663 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$TargetValue</span> < <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3677 3664 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
|
|
|
3678 3665 <span class="s">}</span>
|
|
|
3679 3666 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^>/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3680 3667 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^>=/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3681 3668 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^>=//</span><span class="sc">;</span>
|
|
|
3682 3669 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> >= <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3683 3670 <span class="s">}</span>
|
|
|
3684 3671 <span class="k">else</span> <span class="s">{</span>
|
|
|
3685 3672 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^>//</span><span class="sc">;</span>
|
|
|
3686 3673 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> > <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3687 3674 <span class="s">}</span>
|
|
|
3688 3675 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
|
|
|
3689 3676 <span class="s">}</span>
|
|
|
3690 3677 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^</</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3691 3678 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^<=/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3692 3679 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^<=//</span><span class="sc">;</span>
|
|
|
3693 3680 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> <= <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3694 3681 <span class="s">}</span>
|
|
|
3695 3682 <span class="k">else</span> <span class="s">{</span>
|
|
|
3696 3683 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^<//</span><span class="sc">;</span>
|
|
|
3697 3684 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> < <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3698 3685 <span class="s">}</span>
|
|
|
3699 3686 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
|
|
|
3700 3687 <span class="s">}</span>
|
|
|
3701 3688 <span class="c"># Default is do perform an equality match...</span>
|
|
|
3702 3689 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> == <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3703 3690 <span class="s">}</span>
|
|
|
3704 3691
|
|
|
3705 3692 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
3706 3693 <span class="s">}</span>
|
|
|
3707 3694
|
|
|
3708 3695 <span class="c"># Check whether atoms match bond specifications...</span>
|
|
|
3709 3696 <span class="c">#</span>
|
|
|
3710 <a name="_DoesBondSpecificationMatch-"></a>3697 <span class="k">sub </span><span class="m">_DoesBondSpecificationMatch</span> <span class="s">{</span>
|
|
|
3711 3698 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondSpecificationToMatch</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3712 3699 <span class="k">my</span><span class="s">(</span><span class="i">$BondSpecification</span><span class="cm">,</span> <span class="i">$BondSymbolSpecification</span><span class="cm">,</span> <span class="i">$BondSpecificationMatched</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3713 3700
|
|
|
3714 3701 <span class="c"># Anything to match...</span>
|
|
|
3715 3702 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$BondSpecificationToMatch</span><span class="s">)</span> && <span class="i">$BondSpecificationToMatch</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3716 3703 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3717 3704 <span class="s">}</span>
|
|
|
3718 3705
|
|
|
3719 3706 <span class="c"># Take out any spaces...</span>
|
|
|
3720 3707 <span class="i">$BondSpecificationToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
3721 3708
|
|
|
3722 3709 <span class="c"># Match specified bond specifications. For multiple bond specifications in a comma delimited string,</span>
|
|
|
3723 3710 <span class="c"># only one bond specification needs to match for a successful match...</span>
|
|
|
3724 3711 <span class="c">#</span>
|
|
|
3725 3712 <span class="k">for</span> <span class="i">$BondSpecification</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$BondSpecificationToMatch</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3726 3713 <span class="i">$BondSpecificationMatched</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3727 3714
|
|
|
3728 3715 <span class="c"># Match all specified bond symbol specifications...</span>
|
|
|
3729 3716 <span class="j">BONDSYMBOL:</span> <span class="k">for</span> <span class="i">$BondSymbolSpecification</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$BondSpecification</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3730 3717 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_MatchBondSymbolSpecification</span><span class="s">(</span><span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondSymbolSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3731 3718 <span class="c"># No need to match other bond symbol specifications...</span>
|
|
|
3732 3719 <span class="i">$BondSpecificationMatched</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3733 3720 <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span>
|
|
|
3734 3721 <span class="s">}</span>
|
|
|
3735 3722 <span class="s">}</span>
|
|
|
3736 3723 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSpecificationMatched</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3737 3724 <span class="c"># No need to try matching other bond specifications...</span>
|
|
|
3738 3725 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3739 3726 <span class="s">}</span>
|
|
|
3740 3727 <span class="s">}</span>
|
|
|
3741 3728
|
|
|
3742 3729 <span class="c"># Nothing matched...</span>
|
|
|
3743 3730 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3744 3731 <span class="s">}</span>
|
|
|
3745 3732
|
|
|
3746 3733 <span class="c"># Check whether atoms match bond symbol specification...</span>
|
|
|
3747 3734 <span class="c">#</span>
|
|
|
3748 <a name="_MatchBondSymbolSpecification-"></a>3735 <span class="k">sub </span><span class="m">_MatchBondSymbolSpecification</span> <span class="s">{</span>
|
|
|
3749 3736 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondSymbolSpecification</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3750 3737 <span class="k">my</span><span class="s">(</span><span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondSymbol</span><span class="cm">,</span> <span class="i">$UnknownBondSymbol</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3751 3738
|
|
|
3752 3739 <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$UnknownBondSymbol</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
|
|
|
3753 3740
|
|
|
3754 3741 <span class="c"># Does match needs to be negated?</span>
|
|
|
3755 3742 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbolSpecification</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3756 3743 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3757 3744 <span class="i">$BondSymbolSpecification</span> =~ <span class="q">s/^!//</span><span class="sc">;</span>
|
|
|
3758 3745 <span class="s">}</span>
|
|
|
3759 3746 <span class="i">$BondSymbol</span> = <span class="i">$BondSymbolSpecification</span><span class="sc">;</span>
|
|
|
3760 3747 <span class="i">$Bond</span> = <span class="i">$This</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="i">$BondedAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3761 3748
|
|
|
3762 3749 <span class="j">BONDSYMBOL:</span> <span class="s">{</span>
|
|
|
3763 3750 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(-|1|s|Single)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">->IsSingle</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
3764 3751 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(=|2|d|Double)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">->IsDouble</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
3765 3752 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(#|3|t|Triple)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">->IsTriple</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
3766 3753 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(:|a|Ar|Aromatic)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
3767 3754
|
|
|
3768 3755 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(\@|RB|Ring)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
3769 3756
|
|
|
3770 3757 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(\~|\*|Any)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
3771 3758
|
|
|
3772 3759 <span class="i">$UnknownBondSymbol</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
3773 3760 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_MatchBondSpecification: Unknown bond specification $BondSymbolSpecification..."</span><span class="sc">;</span>
|
|
|
3774 3761 <span class="s">}</span>
|
|
|
3775 3762
|
|
|
3776 3763 <span class="k">if</span> <span class="s">(</span>!<span class="i">$UnknownBondSymbol</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3777 3764 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3778 3765 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3779 3766 <span class="s">}</span>
|
|
|
3780 3767 <span class="s">}</span>
|
|
|
3781 3768
|
|
|
3782 3769 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
3783 3770 <span class="s">}</span>
|
|
|
3784 3771
|
|
|
3785 3772 <span class="c"># Is it a saturated atom?</span>
|
|
|
3786 3773 <span class="c">#</span>
|
|
|
3787 <a name="IsSaturated-"></a>3774 <span class="k">sub </span><span class="m">IsSaturated</span> <span class="s">{</span>
|
|
|
3788 3775 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3789 3776
|
|
|
3790 3777 <span class="k">return</span> !<span class="i">$This</span><span class="i">->IsUnsaturated</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3791 3778 <span class="s">}</span>
|
|
|
3792 3779
|
|
|
3793 3780 <span class="c"># Is it an unsaturated atom containing at least one non-single bond?</span>
|
|
|
3794 3781 <span class="c">#</span>
|
|
|
3795 <a name="IsUnsaturated-"></a>3782 <span class="k">sub </span><span class="m">IsUnsaturated</span> <span class="s">{</span>
|
|
|
3796 3783 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3797 3784 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3798 3785
|
|
|
3799 3786 <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetNumOfBondTypesToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3800 3787
|
|
|
3801 3788 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfDoubleBonds</span> || <span class="i">$NumOfTripleBonds</span> || <span class="i">$NumOfAromaticBonds</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3802 3789 <span class="s">}</span>
|
|
|
3803 3790
|
|
|
3804 3791 <span class="c"># Is atom in a ring?</span>
|
|
|
3805 3792 <span class="c">#</span>
|
|
|
3806 <a name="IsInRing-"></a>3793 <span class="k">sub </span><span class="m">IsInRing</span> <span class="s">{</span>
|
|
|
3807 3794 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3808 3795
|
|
|
3809 3796 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3810 3797 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3811 3798 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3812 3799 <span class="s">}</span>
|
|
|
3813 3800 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3814 3801 <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>
|
|
|
3815 3802
|
|
|
3816 3803 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3817 3804 <span class="s">}</span>
|
|
|
3818 3805
|
|
|
3819 3806 <span class="c"># Is atom not in a ring?</span>
|
|
|
3820 3807 <span class="c">#</span>
|
|
|
3821 <a name="IsNotInRing-"></a>3808 <span class="k">sub </span><span class="m">IsNotInRing</span> <span class="s">{</span>
|
|
|
3822 3809 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3823 3810
|
|
|
3824 3811 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3825 3812 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
3826 3813 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3827 3814 <span class="s">}</span>
|
|
|
3828 3815 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3829 3816 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3830 3817
|
|
|
3831 3818 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomNotInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3832 3819 <span class="s">}</span>
|
|
|
3833 3820
|
|
|
3834 3821 <span class="c"># Is atom only in one ring?</span>
|
|
|
3835 3822 <span class="c">#</span>
|
|
|
3836 <a name="IsOnlyInOneRing-"></a>3823 <span class="k">sub </span><span class="m">IsOnlyInOneRing</span> <span class="s">{</span>
|
|
|
3837 3824 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3838 3825
|
|
|
3839 3826 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3840 3827 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3841 3828 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3842 3829 <span class="s">}</span>
|
|
|
3843 3830 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3844 3831 <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>
|
|
|
3845 3832
|
|
|
3846 3833 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomInOnlyOneRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3847 3834 <span class="s">}</span>
|
|
|
3848 3835
|
|
|
3849 3836 <span class="c"># Is atom in a ring of specific size?</span>
|
|
|
3850 3837 <span class="c">#</span>
|
|
|
3851 <a name="IsInRingOfSize-"></a>3838 <span class="k">sub </span><span class="m">IsInRingOfSize</span> <span class="s">{</span>
|
|
|
3852 3839 <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>
|
|
|
3853 3840
|
|
|
3854 3841 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3855 3842 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3856 3843 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3857 3844 <span class="s">}</span>
|
|
|
3858 3845 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3859 3846 <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>
|
|
|
3860 3847
|
|
|
3861 3848 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomInRingOfSize</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3862 3849 <span class="s">}</span>
|
|
|
3863 3850
|
|
|
3864 3851 <span class="c"># Get size of smallest ring containing the atom...</span>
|
|
|
3865 3852 <span class="c">#</span>
|
|
|
3866 <a name="GetSizeOfSmallestRing-"></a>3853 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span>
|
|
|
3867 3854 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3868 3855
|
|
|
3869 3856 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3870 3857 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3871 3858 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3872 3859 <span class="s">}</span>
|
|
|
3873 3860 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3874 3861 <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>
|
|
|
3875 3862
|
|
|
3876 3863 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfSmallestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3877 3864 <span class="s">}</span>
|
|
|
3878 3865
|
|
|
3879 3866 <span class="c"># Get size of largest ring containing the atom...</span>
|
|
|
3880 3867 <span class="c">#</span>
|
|
|
3881 <a name="GetSizeOfLargestRing-"></a>3868 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span>
|
|
|
3882 3869 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3883 3870
|
|
|
3884 3871 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3885 3872 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
3886 3873 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3887 3874 <span class="s">}</span>
|
|
|
3888 3875 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3889 3876 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3890 3877
|
|
|
3891 3878 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfLargestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3892 3879 <span class="s">}</span>
|
|
|
3893 3880
|
|
|
3894 3881 <span class="c"># Get number of rings containing the atom...</span>
|
|
|
3895 3882 <span class="c">#</span>
|
|
|
3896 <a name="GetNumOfRings-"></a>3883 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span>
|
|
|
3897 3884 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3898 3885
|
|
|
3899 3886 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3900 3887 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3901 3888 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3902 3889 <span class="s">}</span>
|
|
|
3903 3890 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3904 3891 <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>
|
|
|
3905 3892
|
|
|
3906 3893 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3907 3894 <span class="s">}</span>
|
|
|
3908 3895
|
|
|
3909 3896 <span class="c"># Get number of rings with odd size containing the atom...</span>
|
|
|
3910 3897 <span class="c">#</span>
|
|
|
3911 <a name="GetNumOfRingsWithOddSize-"></a>3898 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span>
|
|
|
3912 3899 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3913 3900
|
|
|
3914 3901 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3915 3902 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
3916 3903 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3917 3904 <span class="s">}</span>
|
|
|
3918 3905 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3919 3906 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3920 3907
|
|
|
3921 3908 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3922 3909 <span class="s">}</span>
|
|
|
3923 3910
|
|
|
3924 3911 <span class="c"># Get number of rings with even size containing the atom...</span>
|
|
|
3925 3912 <span class="c">#</span>
|
|
|
3926 <a name="GetNumOfRingsWithEvenSize-"></a>3913 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span>
|
|
|
3927 3914 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3928 3915
|
|
|
3929 3916 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3930 3917 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3931 3918 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3932 3919 <span class="s">}</span>
|
|
|
3933 3920 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3934 3921 <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>
|
|
|
3935 3922
|
|
|
3936 3923 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3937 3924 <span class="s">}</span>
|
|
|
3938 3925
|
|
|
3939 3926 <span class="c"># Get number of rings with specified size containing the atom...</span>
|
|
|
3940 3927 <span class="c">#</span>
|
|
|
3941 <a name="GetNumOfRingsWithSize-"></a>3928 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span>
|
|
|
3942 3929 <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>
|
|
|
3943 3930
|
|
|
3944 3931 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3945 3932 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3946 3933 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3947 3934 <span class="s">}</span>
|
|
|
3948 3935 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3949 3936 <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>
|
|
|
3950 3937
|
|
|
3951 3938 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithSize</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3952 3939
|
|
|
3953 3940 <span class="s">}</span>
|
|
|
3954 3941
|
|
|
3955 3942 <span class="c"># Get number of rings with size less than specified containing the atom...</span>
|
|
|
3956 3943 <span class="c">#</span>
|
|
|
3957 <a name="GetNumOfRingsWithSizeLessThan-"></a>3944 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span>
|
|
|
3958 3945 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3959 3946
|
|
|
3960 3947 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3961 3948 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
3962 3949 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3963 3950 <span class="s">}</span>
|
|
|
3964 3951 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3965 3952 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3966 3953
|
|
|
3967 3954 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithSizeLessThan</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>
|
|
|
3968 3955 <span class="s">}</span>
|
|
|
3969 3956
|
|
|
3970 3957 <span class="c"># Get number of rings with size greater than specified size containing the atom...</span>
|
|
|
3971 3958 <span class="c">#</span>
|
|
|
3972 <a name="GetNumOfRingsWithSizeGreaterThan-"></a>3959 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span>
|
|
|
3973 3960 <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>
|
|
|
3974 3961
|
|
|
3975 3962 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3976 3963 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3977 3964 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3978 3965 <span class="s">}</span>
|
|
|
3979 3966 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3980 3967 <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>
|
|
|
3981 3968
|
|
|
3982 3969 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithSizeGreaterThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3983 3970 <span class="s">}</span>
|
|
|
3984 3971
|
|
|
3985 3972 <span class="c"># Get all rings an array of references to arrays containing ring atoms...</span>
|
|
|
3986 3973 <span class="c">#</span>
|
|
|
3987 <a name="GetRings-"></a>3974 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span>
|
|
|
3988 3975 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3989 3976
|
|
|
3990 3977 <span class="c"># Is this atom in a molecule?</span>
|
|
|
3991 3978 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3992 3979 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
3993 3980 <span class="s">}</span>
|
|
|
3994 3981 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3995 3982 <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>
|
|
|
3996 3983
|
|
|
3997 3984 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3998 3985 <span class="s">}</span>
|
|
|
3999 3986
|
|
|
4000 3987 <span class="c"># Get smallest ring as an array containing ring atoms...</span>
|
|
|
4001 3988 <span class="c">#</span>
|
|
|
4002 <a name="GetSmallestRing-"></a>3989 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span>
|
|
|
4003 3990 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4004 3991
|
|
|
4005 3992 <span class="c"># Is this atom in a molecule?</span>
|
|
|
4006 3993 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
4007 3994 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
4008 3995 <span class="s">}</span>
|
|
|
4009 3996 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4010 3997 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4011 3998
|
|
|
4012 3999 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSmallestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4013 4000 <span class="s">}</span>
|
|
|
4014 4001
|
|
|
4015 4002 <span class="c"># Get largest ring as an array containing ring atoms...</span>
|
|
|
4016 4003 <span class="c">#</span>
|
|
|
4017 <a name="GetLargestRing-"></a>4004 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span>
|
|
|
4018 4005 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4019 4006
|
|
|
4020 4007 <span class="c"># Is this atom in a molecule?</span>
|
|
|
4021 4008 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4022 4009 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
4023 4010 <span class="s">}</span>
|
|
|
4024 4011 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4025 4012 <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>
|
|
|
4026 4013
|
|
|
4027 4014 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetLargestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4028 4015 <span class="s">}</span>
|
|
|
4029 4016
|
|
|
4030 4017 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span>
|
|
|
4031 4018 <span class="c">#</span>
|
|
|
4032 <a name="GetRingsWithOddSize-"></a>4019 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span>
|
|
|
4033 4020 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4034 4021
|
|
|
4035 4022 <span class="c"># Is this atom in a molecule?</span>
|
|
|
4036 4023 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
4037 4024 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
4038 4025 <span class="s">}</span>
|
|
|
4039 4026 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4040 4027 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4041 4028
|
|
|
4042 4029 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4043 4030 <span class="s">}</span>
|
|
|
4044 4031
|
|
|
4045 4032 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span>
|
|
|
4046 4033 <span class="c">#</span>
|
|
|
4047 <a name="GetRingsWithEvenSize-"></a>4034 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span>
|
|
|
4048 4035 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4049 4036
|
|
|
4050 4037 <span class="c"># Is this atom in a molecule?</span>
|
|
|
4051 4038 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4052 4039 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
4053 4040 <span class="s">}</span>
|
|
|
4054 4041 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4055 4042 <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>
|
|
|
4056 4043
|
|
|
4057 4044 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4058 4045 <span class="s">}</span>
|
|
|
4059 4046
|
|
|
4060 4047 <span class="c"># Get rings with specified size as an array of references to arrays containing ring atoms...</span>
|
|
|
4061 4048 <span class="c">#</span>
|
|
|
4062 <a name="GetRingsWithSize-"></a>4049 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span>
|
|
|
4063 4050 <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>
|
|
|
4064 4051
|
|
|
4065 4052 <span class="c"># Is this atom in a molecule?</span>
|
|
|
4066 4053 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4067 4054 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
4068 4055 <span class="s">}</span>
|
|
|
4069 4056 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4070 4057 <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>
|
|
|
4071 4058
|
|
|
4072 4059 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithSize</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4073 4060 <span class="s">}</span>
|
|
|
4074 4061
|
|
|
4075 4062 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span>
|
|
|
4076 4063 <span class="c">#</span>
|
|
|
4077 <a name="GetRingsWithSizeLessThan-"></a>4064 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span>
|
|
|
4078 4065 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4079 4066
|
|
|
4080 4067 <span class="c"># Is this atom in a molecule?</span>
|
|
|
4081 4068 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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>
|
|
|
4082 4069 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
4083 4070 <span class="s">}</span>
|
|
|
4084 4071 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4085 4072 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4086 4073
|
|
|
4087 4074 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithSizeLessThan</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>
|
|
|
4088 4075 <span class="s">}</span>
|
|
|
4089 4076
|
|
|
4090 4077 <span class="c"># Get rings with size greater than specfied size as an array of references to arrays containing ring atoms...</span>
|
|
|
4091 4078 <span class="c">#</span>
|
|
|
4092 <a name="GetRingsWithSizeGreaterThan-"></a>4079 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span>
|
|
|
4093 4080 <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>
|
|
|
4094 4081
|
|
|
4095 4082 <span class="c"># Is this atom in a molecule?</span>
|
|
|
4096 4083 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4097 4084 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
4098 4085 <span class="s">}</span>
|
|
|
4099 4086 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4100 4087 <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>
|
|
|
4101 4088
|
|
|
4102 4089 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithSizeGreaterThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4103 4090 <span class="s">}</span>
|
|
|
4104 4091
|
|
|
4105 4092 <span class="c"># Get next object ID...</span>
|
|
|
4106 <a name="_GetNewObjectID-"></a>4093 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span>
|
|
|
4107 4094 <span class="i">$ObjectID</span>++<span class="sc">;</span>
|
|
|
4108 4095 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span>
|
|
|
4109 4096 <span class="s">}</span>
|
|
|
4110 4097
|
|
|
4111 4098 <span class="c"># Return a string containing vertices, edges and other properties...</span>
|
|
|
4112 <a name="StringifyAtom-"></a>4099 <span class="k">sub </span><span class="m">StringifyAtom</span> <span class="s">{</span>
|
|
|
4113 4100 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4114 4101 <span class="k">my</span><span class="s">(</span><span class="i">$AtomString</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$XYZVector</span><span class="cm">,</span> <span class="i">$AtomicWeight</span><span class="cm">,</span> <span class="i">$ExactMass</span><span class="cm">,</span> <span class="i">$NumOfNeighbors</span><span class="cm">,</span> <span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$Valence</span><span class="cm">,</span> <span class="i">$MissingHydrogens</span><span class="cm">,</span> <span class="i">$TotalHydrogens</span><span class="cm">,</span> <span class="i">$ImplicitHydrogens</span><span class="cm">,</span> <span class="i">$ExplicitHydrogens</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="cm">,</span> <span class="i">$FreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$StereoCenter</span><span class="cm">,</span> <span class="i">$StereoCenterStatus</span><span class="cm">,</span> <span class="i">$StereoChemistry</span><span class="cm">,</span> <span class="i">$StereochemistryString</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$NumOfRings</span><span class="cm">,</span> <span class="i">$AromaticAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4115 4102
|
|
|
4116 4103 <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>
|
|
|
4117 4104 <span class="i">$Name</span> = <span class="i">$This</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4118 4105 <span class="i">$AtomSymbol</span> = <span class="i">$This</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4119 4106 <span class="i">$AtomicNumber</span> = <span class="i">$This</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4120 4107 <span class="i">$XYZVector</span> = <span class="i">$This</span><span class="i">->GetXYZVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4121 4108
|
|
|
4122 4109 <span class="i">$AtomicWeight</span> = <span class="i">$This</span><span class="i">->GetAtomicWeight</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4123 4110 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$AtomicWeight</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4124 4111 <span class="i">$AtomicWeight</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4125 4112 <span class="s">}</span>
|
|
|
4126 4113 <span class="i">$ExactMass</span> = <span class="i">$This</span><span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4127 4114 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExactMass</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4128 4115 <span class="i">$ExactMass</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4129 4116 <span class="s">}</span>
|
|
|
4130 4117 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">->GetNumOfNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4131 4118 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4132 4119 <span class="i">$NumOfNeighbors</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4133 4120 <span class="s">}</span>
|
|
|
4134 4121 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4135 4122 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4136 4123 <span class="i">$NumOfBonds</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4137 4124 <span class="s">}</span>
|
|
|
4138 4125 <span class="i">$Valence</span> = <span class="i">$This</span><span class="i">->GetValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4139 4126 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Valence</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4140 4127 <span class="i">$Valence</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4141 4128 <span class="s">}</span>
|
|
|
4142 4129
|
|
|
4143 4130 <span class="i">$MissingHydrogens</span> = <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4144 4131 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$MissingHydrogens</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4145 4132 <span class="i">$MissingHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4146 4133 <span class="s">}</span>
|
|
|
4147 4134 <span class="i">$TotalHydrogens</span> = <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4148 4135 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$TotalHydrogens</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4149 4136 <span class="i">$TotalHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4150 4137 <span class="s">}</span>
|
|
|
4151 4138 <span class="i">$ImplicitHydrogens</span> = <span class="i">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4152 4139 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ImplicitHydrogens</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4153 4140 <span class="i">$ImplicitHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4154 4141 <span class="s">}</span>
|
|
|
4155 4142 <span class="i">$ExplicitHydrogens</span> = <span class="i">$This</span><span class="i">->GetNumOfExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4156 4143 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExplicitHydrogens</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4157 4144 <span class="i">$ExplicitHydrogens</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4158 4145 <span class="s">}</span>
|
|
|
4159 4146
|
|
|
4160 4147 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4161 4148 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$FormalCharge</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4162 4149 <span class="i">$FormalCharge</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4163 4150 <span class="s">}</span>
|
|
|
4164 4151 <span class="i">$Charge</span> = <span class="i">$This</span><span class="i">->GetCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4165 4152 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4166 4153 <span class="i">$Charge</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4167 4154 <span class="s">}</span>
|
|
|
4168 4155
|
|
|
4169 4156 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4170 4157 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SpinMultiplicity</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4171 4158 <span class="i">$SpinMultiplicity</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4172 4159 <span class="s">}</span>
|
|
|
4173 4160 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4174 4161 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$FreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4175 4162 <span class="i">$FreeRadicalElectrons</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4176 4163 <span class="s">}</span>
|
|
|
4177 4164
|
|
|
4178 4165 <span class="i">$RingAtom</span> = <span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4179 4166 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$RingAtom</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4180 4167 <span class="i">$RingAtom</span> = <span class="i">$RingAtom</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span>
|
|
|
4181 4168 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4182 4169 <span class="s">}</span>
|
|
|
4183 4170 <span class="k">else</span> <span class="s">{</span>
|
|
|
4184 4171 <span class="i">$RingAtom</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4185 4172 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4186 4173 <span class="s">}</span>
|
|
|
4187 4174
|
|
|
4188 4175 <span class="i">$AromaticAtom</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4189 4176 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticAtom</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4190 4177 <span class="i">$AromaticAtom</span> = <span class="i">$AromaticAtom</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span>
|
|
|
4191 4178 <span class="s">}</span>
|
|
|
4192 4179 <span class="k">else</span> <span class="s">{</span>
|
|
|
4193 4180 <span class="i">$AromaticAtom</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4194 4181 <span class="s">}</span>
|
|
|
4195 4182
|
|
|
4196 4183 <span class="i">$StereochemistryString</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
4197 4184 <span class="i">$StereoCenter</span> = <span class="i">$This</span><span class="i">->GetStereoCenter</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4198 4185 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$StereoCenter</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4199 4186 <span class="i">$StereoCenterStatus</span> = <span class="i">$This</span><span class="i">->IsStereoCenter</span><span class="s">(</span><span class="s">)</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span>
|
|
|
4200 4187 <span class="i">$StereoChemistry</span> = <span class="i">$This</span><span class="i">->GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4201 4188 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$StereoChemistry</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4202 4189 <span class="i">$StereoChemistry</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4203 4190 <span class="s">}</span>
|
|
|
4204 4191 <span class="i">$StereochemistryString</span> = <span class="q">"StereoCenter: $StereoCenterStatus; Stereochemistry: $StereoChemistry"</span><span class="sc">;</span>
|
|
|
4205 4192 <span class="s">}</span>
|
|
|
4206 4193
|
|
|
4207 4194 <span class="i">$AtomString</span> = <span class="q">"Atom: ID: $ID; Name: \"$Name\"; AtomSymbol: \"$AtomSymbol\"; AtomicNumber: $AtomicNumber; XYZ: $XYZVector; AtomicWeight: $AtomicWeight; ExactMass: $ExactMass; NumOfNeighbors: $NumOfNeighbors; NumOfBonds: $NumOfBonds; Valence: $Valence; MissingHydrogens: $MissingHydrogens; TotalHydrogens: $TotalHydrogens; ImplicitHydrogens: $ImplicitHydrogens; ExplicitHydrogens: $ExplicitHydrogens; FormalCharge: $FormalCharge; Charge: $Charge; SpinMultiplicity: $SpinMultiplicity; FreeRadicalElectrons: $FreeRadicalElectrons; RingAtom: $RingAtom; NumOfAtomRings: $NumOfRings; AromaticAtom: $AromaticAtom"</span><span class="sc">;</span>
|
|
|
4208 4195
|
|
|
4209 4196 <span class="k">if</span> <span class="s">(</span><span class="i">$StereochemistryString</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4210 4197 <span class="i">$AtomString</span> .= <span class="q">"; $StereochemistryString"</span><span class="sc">;</span>
|
|
|
4211 4198 <span class="s">}</span>
|
|
|
4212 4199
|
|
|
4213 4200 <span class="k">return</span> <span class="i">$AtomString</span><span class="sc">;</span>
|
|
|
4214 4201 <span class="s">}</span>
|
|
|
4215 4202
|
|
|
4216 4203 <span class="c"># Load appropriate atom data files from <MayaChemTools>/lib directory used by various</span>
|
|
|
4217 4204 <span class="c"># object methods in the current class...</span>
|
|
|
4218 4205 <span class="c">#</span>
|
|
|
4219 <a name="_LoadAtomClassData-"></a>4206 <span class="k">sub </span><span class="m">_LoadAtomClassData</span> <span class="s">{</span>
|
|
|
4220 4207 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4221 4208
|
|
|
4222 4209 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4223 4210
|
|
|
4224 4211 <span class="i">_LoadAtomValenceModelData</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4225 4212
|
|
|
4226 4213 <span class="s">}</span>
|
|
|
4227 4214
|
|
|
4228 4215 <span class="c">#</span>
|
|
|
4229 4216 <span class="c"># Load data for supported valence models...</span>
|
|
|
4230 4217 <span class="c">#</span>
|
|
|
4231 <a name="_LoadAtomValenceModelData-"></a>4218 <span class="k">sub </span><span class="m">_LoadAtomValenceModelData</span> <span class="s">{</span>
|
|
|
4232 4219 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4233 4220 <span class="k">my</span><span class="s">(</span><span class="i">$MDLValenceModelDataFile</span><span class="cm">,</span> <span class="i">$DaylightValenceModelDataFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4234 4221
|
|
|
4235 4222 <span class="i">%MDLValenceModelDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4236 4223 <span class="i">%DaylightValenceModelDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4237 4224
|
|
|
4238 4225 <span class="i">$MDLValenceModelDataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">"/data/MDLValenceModelData.csv"</span><span class="sc">;</span>
|
|
|
4239 4226 <span class="i">$DaylightValenceModelDataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">"/data/DaylightValenceModelData.csv"</span><span class="sc">;</span>
|
|
|
4240 4227
|
|
|
4241 4228 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$MDLValenceModelDataFile"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4242 4229 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAtomValenceModelData: MayaChemTools package file, $MDLValenceModelDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span>
|
|
|
4243 4230 <span class="s">}</span>
|
|
|
4244 4231
|
|
|
4245 4232 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$DaylightValenceModelDataFile"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4246 4233 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAtomValenceModelData: MayaChemTools package file, $DaylightValenceModelDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span>
|
|
|
4247 4234 <span class="s">}</span>
|
|
|
4248 4235
|
|
|
4249 4236 <span class="i">_LoadValenceModelDataFile</span><span class="s">(</span><span class="i">$MDLValenceModelDataFile</span><span class="cm">,</span> \<span class="i">%MDLValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4250 4237 <span class="i">_LoadValenceModelDataFile</span><span class="s">(</span><span class="i">$DaylightValenceModelDataFile</span><span class="cm">,</span> \<span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4251 4238
|
|
|
4252 4239 <span class="s">}</span>
|
|
|
4253 4240
|
|
|
4254 4241 <span class="c">#</span>
|
|
|
4255 4242 <span class="c"># Load valence model data file...</span>
|
|
|
4256 4243 <span class="c">#</span>
|
|
|
4257 <a name="_LoadValenceModelDataFile-"></a>4244 <span class="k">sub </span><span class="m">_LoadValenceModelDataFile</span> <span class="s">{</span>
|
|
|
4258 4245 <span class="k">my</span><span class="s">(</span><span class="i">$DataFile</span><span class="cm">,</span> <span class="i">$DataMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4259 4246
|
|
|
4260 4247 <span class="c"># File format:</span>
|
|
|
4261 4248 <span class="c">#</span>
|
|
|
4262 4249 <span class="c"># "AtomicNumber","ElementSymbol","FormalCharge","CommomValences"</span>
|
|
|
4263 4250 <span class="c">#</span>
|
|
|
4264 4251 <span class="k">my</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4265 4252
|
|
|
4266 4253 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span>
|
|
|
4267 4254 <span class="k">open</span> <span class="w">DATAFILE</span><span class="cm">,</span> <span class="q">"$DataFile"</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">"Couldn't open $DataFile: $! ..."</span><span class="sc">;</span>
|
|
|
4268 4255
|
|
|
4269 4256 <span class="c"># Skip lines up to column labels...</span>
|
|
|
4270 4257 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4271 4258 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4272 4259 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
4273 4260 <span class="s">}</span>
|
|
|
4274 4261 <span class="s">}</span>
|
|
|
4275 4262 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4276 4263 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span>
|
|
|
4277 4264
|
|
|
4278 4265 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4279 4266
|
|
|
4280 4267 <span class="c"># Process element data...</span>
|
|
|
4281 4268 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4282 4269 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4283 4270 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
4284 4271 <span class="s">}</span>
|
|
|
4285 4272 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4286 4273 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4287 4274 <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4288 4275 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadValenceModelDataFile: The number of data fields, @LineWords, in $DataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span>
|
|
|
4289 4276 <span class="s">}</span>
|
|
|
4290 4277
|
|
|
4291 4278 <span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="s">)</span> = <span class="i">@LineWords</span><span class="sc">;</span>
|
|
|
4292 4279
|
|
|
4293 4280 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4294 4281 <span class="c"># Additional data for an element...</span>
|
|
|
4295 4282 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4296 4283 <span class="c"># Duplicate data entries for an element...</span>
|
|
|
4297 4284 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}::_LoadValenceModelDataFile: Ignoring valence data for element with atomic number $AtomicNumber and formal charge $FormalCharge in data file $DataFile: It has already been loaded.\nLine: $Line..."</span><span class="sc">;</span>
|
|
|
4298 4285 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
4299 4286 <span class="s">}</span>
|
|
|
4300 4287 <span class="s">}</span>
|
|
|
4301 4288 <span class="k">else</span> <span class="s">{</span>
|
|
|
4302 4289 <span class="c"># Data for a new element...</span>
|
|
|
4303 4290 <span class="i">%</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4304 4291 <span class="s">}</span>
|
|
|
4305 4292
|
|
|
4306 4293 <span class="i">%</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4307 4294 <span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">ElementSymbol</span>} = <span class="i">$ElementSymbol</span><span class="sc">;</span>
|
|
|
4308 4295
|
|
|
4309 4296 <span class="i">@</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">CommonValences</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4310 4297 <span class="i">@</span>{<span class="i">$DataMapRef</span>->{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">CommonValences</span>}} = <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="sc">;</span>
|
|
|
4311 4298 <span class="s">}</span>
|
|
|
4312 4299 <span class="k">close</span> <span class="w">DATAFILE</span><span class="sc">;</span>
|
|
|
4313 4300 <span class="s">}</span>
|
|
|
4314 4301
|
|
|
4315 <a name="EOF-"></a></pre>
|
|
|
4316 <p> </p>
|
|
|
4317 <br />
|
|
|
4318 <center>
|
|
|
4319 <img src="../../../images/h2o2.png">
|
|
|
4320 </center>
|
|
|
4321 </body>
|
|
|
4322 </html>
|
