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3 <title>MayaChemTools:Code:FileIO::MDLMolFileIO.pm</title>
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13 <pre>
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14 <a name="package-FileIO::MDLMolFileIO-"></a> 1 <span class="k">package </span><span class="i">FileIO::MDLMolFileIO</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: MDLMolFileIO.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:48:43 $</span>
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18 5 <span class="c"># $Revision: 1.32 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">SDFileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">FileIO::FileIO</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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51 38
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52 39 <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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53 40
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54 41 <span class="i">@ISA</span> = <span class="q">qw(FileIO::FileIO Exporter)</span><span class="sc">;</span>
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55 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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56 43 <span class="i">@EXPORT_OK</span> = <span class="q">qw(IsMDLMolFile)</span><span class="sc">;</span>
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57 44
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58 45 <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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59 46
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60 47 <span class="c"># Setup class variables...</span>
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61 48 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
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62 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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63 50
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64 51 <span class="c"># Class constructor...</span>
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65 <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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66 53 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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67 54
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68 55 <span class="c"># Initialize object...</span>
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69 56 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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70 57 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span>
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71 58 <span class="i">$This</span><span class="i">->_InitializeMDLMolFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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72 59
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73 60 <span class="i">$This</span><span class="i">->_InitializeMDLMolFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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74 61
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75 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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76 63 <span class="s">}</span>
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77 64
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78 65 <span class="c"># Initialize any local object data...</span>
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79 66 <span class="c">#</span>
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80 <a name="_InitializeMDLMolFileIO-"></a> 67 <span class="k">sub </span><span class="m">_InitializeMDLMolFileIO</span> <span class="s">{</span>
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81 68 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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82 69
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83 70 <span class="c"># Nothing to do: Base class FileIO handles default class variables...</span>
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84 71
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85 72 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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86 73 <span class="s">}</span>
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87 74
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88 75 <span class="c"># Initialize class ...</span>
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89 <a name="_InitializeClass-"></a> 76 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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90 77 <span class="c">#Class name...</span>
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91 78 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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92 79
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93 80 <span class="s">}</span>
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94 81
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95 82 <span class="c"># Initialize object values...</span>
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96 <a name="_InitializeMDLMolFileIOProperties-"></a> 83 <span class="k">sub </span><span class="m">_InitializeMDLMolFileIOProperties</span> <span class="s">{</span>
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97 84 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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98 85
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99 86 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span>
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100 87 <span class="c"># are implemented on-demand using ObjectProperty class.</span>
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101 88
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102 89 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Value</span><span class="s">)</span><span class="sc">;</span>
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106 93 <span class="s">}</span>
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107 94
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108 95 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="s">)</span> <span class="s">{</span>
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109 96 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying file name..."</span><span class="sc">;</span>
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110 97 <span class="s">}</span>
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111 98
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112 99 <span class="c"># Make sure it's a MDLMol file...</span>
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113 100 <span class="i">$Name</span> = <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="sc">;</span>
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114 101 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsMDLMolFile</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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115 102 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $Name, doesn't appear to be MDLMol format..."</span><span class="sc">;</span>
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116 103 <span class="s">}</span>
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117 104
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118 105 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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119 106 <span class="s">}</span>
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120 107
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121 108 <span class="c"># Is it a MDLMol file?</span>
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122 <a name="IsMDLMolFile-"></a> 109 <span class="k">sub </span><span class="m">IsMDLMolFile ($;$)</span> <span class="s">{</span>
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123 110 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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124 111 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
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125 112
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126 113 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMDLMolFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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127 114 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FileName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
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128 115 <span class="s">}</span>
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129 116 <span class="k">else</span> <span class="s">{</span>
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130 117 <span class="i">$FileName</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
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131 118 <span class="s">}</span>
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132 119
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133 120 <span class="c"># Check file extension...</span>
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134 121 <span class="i">$Status</span> = <span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"mol"</span><span class="s">)</span><span class="sc">;</span>
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135 122
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136 123 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
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137 124 <span class="s">}</span>
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138 125
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139 126 <span class="c"># Read molecule from file and return molecule object...</span>
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140 <a name="ReadMolecule-"></a> 127 <span class="k">sub </span><span class="m">ReadMolecule</span> <span class="s">{</span>
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141 128 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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142 129 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span>
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143 130
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144 131 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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145 132 <span class="k">return</span> <span class="i">$This</span><span class="i">->ParseMoleculeString</span><span class="s">(</span><span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
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146 133 <span class="s">}</span>
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147 134
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148 135 <span class="c"># Write compound data using Molecule object...</span>
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149 <a name="WriteMolecule-"></a> 136 <span class="k">sub </span><span class="m">WriteMolecule</span> <span class="s">{</span>
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150 137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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151 138
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152 139 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> && <span class="i">$Molecule</span><span class="i">->IsMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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153 140 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->WriteMolecule: No data written: Molecule object is not specified..."</span><span class="sc">;</span>
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154 141 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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155 142 <span class="s">}</span>
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156 143 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span>
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157 144 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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158 145
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159 146 <span class="k">print</span> <span class="i">$FileHandle</span> <span class="i">$This</span><span class="i">->GenerateMoleculeString</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> . <span class="q">"\n"</span><span class="sc">;</span>
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160 147
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161 148 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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162 149 <span class="s">}</span>
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163 150
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164 151 <span class="c"># Retrieve molecule string...</span>
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165 <a name="ReadMoleculeString-"></a> 152 <span class="k">sub </span><span class="m">ReadMoleculeString</span> <span class="s">{</span>
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166 153 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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167 154 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span>
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168 155
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169 156 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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170 157 <span class="k">return</span> <span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span>
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171 158 <span class="s">}</span>
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172 159
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173 160 <span class="c"># Parse molecule string and return molecule object. ParseMoleculeString supports two invocation methods: class</span>
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174 161 <span class="c"># method or a package function.</span>
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175 162 <span class="c">#</span>
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176 <a name="ParseMoleculeString-"></a> 163 <span class="k">sub </span><span class="m">ParseMoleculeString</span> <span class="s">{</span>
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177 164 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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178 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="s">)</span><span class="sc">;</span>
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179 166
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180 167 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMDLMolFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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181 168 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
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182 169 <span class="s">}</span>
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183 170 <span class="k">else</span> <span class="s">{</span>
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184 171 <span class="i">$MoleculeString</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
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185 172 <span class="i">$This</span> = <span class="k">undef</span><span class="sc">;</span>
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186 173 <span class="s">}</span>
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187 174 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MoleculeString</span><span class="s">)</span> <span class="s">{</span>
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188 175 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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189 176 <span class="s">}</span>
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190 177 <span class="k">my</span><span class="s">(</span><span class="i">$LineIndex</span><span class="cm">,</span> <span class="i">@MoleculeLines</span><span class="s">)</span><span class="sc">;</span>
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191 178 <span class="i">@MoleculeLines</span> = <span class="k">split</span> <span class="q">/\n/</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="sc">;</span>
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192 179
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193 180 <span class="c"># Create molecule object and set molecule level native and MDL properties...</span>
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194 181 <span class="c">#</span>
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195 182 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
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196 183 <span class="i">$Molecule</span> = <span class="i">new</span> <span class="i">Molecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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197 184
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198 185 <span class="c"># Set valence model for calculating implicit hydrogens...</span>
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199 186 <span class="i">$Molecule</span><span class="i">->SetValenceModel</span><span class="s">(</span><span class="q">'MDLValenceModel'</span><span class="s">)</span><span class="sc">;</span>
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200 187
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201 188 <span class="c"># Process headers data...</span>
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202 189 <span class="i">$LineIndex</span> = <span class="n">0</span><span class="sc">;</span>
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|
203 190 <span class="k">my</span><span class="s">(</span><span class="i">$MoleculeName</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdMolNameLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span>
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204 191 <span class="i">$MoleculeName</span> = <span class="i">TextUtil::RemoveTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$MoleculeName</span><span class="s">)</span><span class="sc">;</span>
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205 192 <span class="i">$Molecule</span><span class="i">->SetName</span><span class="s">(</span><span class="i">$MoleculeName</span><span class="s">)</span><span class="sc">;</span>
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206 193
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|
207 194 <span class="i">$LineIndex</span>++<span class="sc">;</span>
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|
208 195 <span class="k">my</span><span class="s">(</span><span class="i">$UserInitial</span><span class="cm">,</span> <span class="i">$ProgramName</span><span class="cm">,</span> <span class="i">$Date</span><span class="cm">,</span> <span class="i">$Code</span><span class="cm">,</span> <span class="i">$ScalingFactor1</span><span class="cm">,</span> <span class="i">$ScalingFactor2</span><span class="cm">,</span> <span class="i">$Energy</span><span class="cm">,</span> <span class="i">$RegistryNum</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdMiscInfoLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span>
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209 196 <span class="i">$Molecule</span><span class="i">->SetProperties</span><span class="s">(</span><span class="q">'MDLUserInitial'</span> <span class="cm">=></span> <span class="i">$UserInitial</span><span class="cm">,</span> <span class="q">'MDLProgramName'</span> <span class="cm">=></span> <span class="i">$ProgramName</span><span class="cm">,</span> <span class="q">'MDLDate'</span> <span class="cm">=></span> <span class="i">$Date</span><span class="cm">,</span> <span class="q">'MDLCode'</span> <span class="cm">=></span> <span class="i">$Code</span><span class="cm">,</span> <span class="q">'MDLScalingFactor1'</span> <span class="cm">=></span> <span class="i">$ScalingFactor1</span><span class="cm">,</span> <span class="q">'MDLScalingFactor2'</span> <span class="cm">=></span> <span class="i">$ScalingFactor2</span><span class="cm">,</span> <span class="q">'MDLEnergy'</span> <span class="cm">=></span> <span class="i">$Energy</span><span class="cm">,</span> <span class="q">'MDLRegistryNum'</span> <span class="cm">=></span> <span class="i">$RegistryNum</span><span class="s">)</span><span class="sc">;</span>
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210 197
|
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|
211 198 <span class="i">$LineIndex</span>++<span class="sc">;</span>
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|
|
212 199 <span class="k">my</span><span class="s">(</span><span class="i">$Comments</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdCommentsLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span>
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213 200 <span class="i">$Molecule</span><span class="i">->SetProperties</span><span class="s">(</span><span class="q">'MDLComments'</span> <span class="cm">=></span> <span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span>
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|
214 201
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|
|
215 202 <span class="i">$LineIndex</span>++<span class="sc">;</span>
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|
216 203 <span class="k">my</span><span class="s">(</span><span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$BondCount</span><span class="cm">,</span> <span class="i">$ChiralFlag</span><span class="cm">,</span> <span class="i">$PropertyCount</span><span class="cm">,</span> <span class="i">$Version</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdCountsLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span>
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217 204
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|
218 205 <span class="i">$Molecule</span><span class="i">->SetProperties</span><span class="s">(</span><span class="q">'MDLChiralFlag'</span> <span class="cm">=></span> <span class="i">$ChiralFlag</span><span class="cm">,</span> <span class="q">'MDLPropertyCount'</span> <span class="cm">=></span> <span class="i">$PropertyCount</span><span class="cm">,</span> <span class="q">'MDLVersion'</span> <span class="cm">=></span> <span class="i">$Version</span><span class="s">)</span><span class="sc">;</span>
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219 206
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220 207 <span class="c"># Process atom data...</span>
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221 208 <span class="k">my</span><span class="s">(</span><span class="i">$FirstAtomLineIndex</span><span class="cm">,</span> <span class="i">$LastAtomLineIndex</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
|
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|
222 209
|
|
|
223 210 <span class="i">$AtomNum</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
224 211 <span class="i">%AtomNumToAtomMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
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|
225 212 <span class="i">$FirstAtomLineIndex</span> = <span class="n">4</span><span class="sc">;</span> <span class="i">$LastAtomLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span> - <span class="n">1</span><span class="sc">;</span>
|
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226 213
|
|
|
227 214 <span class="k">for</span> <span class="s">(</span><span class="i">$LineIndex</span> = <span class="i">$FirstAtomLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span> <= <span class="i">$LastAtomLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span>++<span class="s">)</span> <span class="s">{</span>
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|
|
228 215 <span class="i">$AtomNum</span>++<span class="sc">;</span>
|
|
|
229 216 <span class="s">(</span><span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdAtomLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span>
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|
|
230 217
|
|
|
231 218 <span class="i">$Atom</span> = <span class="i">new</span> <span class="i">Atom</span><span class="s">(</span><span class="q">'AtomSymbol'</span> <span class="cm">=></span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="q">'XYZ'</span> <span class="cm">=></span> <span class="s">[</span><span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
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|
|
232 219
|
|
|
233 220 <span class="k">if</span> <span class="s">(</span><span class="i">$MassDifference</span> && <span class="i">$MassDifference</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
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|
|
234 221 <span class="i">_ProcessMassDifference</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="s">)</span><span class="sc">;</span>
|
|
|
235 222 <span class="s">}</span>
|
|
|
236 223 <span class="k">if</span> <span class="s">(</span><span class="i">$Charge</span> && <span class="i">$Charge</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
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|
|
237 224 <span class="i">_ProcessCharge</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
238 225 <span class="s">}</span>
|
|
|
239 226 <span class="k">if</span> <span class="s">(</span><span class="i">$StereoParity</span> && <span class="i">$StereoParity</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
240 227 <span class="i">_ProcessStereoParity</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
241 228 <span class="s">}</span>
|
|
|
242 229
|
|
|
243 230 <span class="i">$AtomNumToAtomMap</span>{<span class="i">$AtomNum</span>} = <span class="i">$Atom</span><span class="sc">;</span>
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|
244 231 <span class="i">$Molecule</span><span class="i">->AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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|
245 232 <span class="s">}</span>
|
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|
246 233
|
|
|
247 234 <span class="c"># Process bond data...</span>
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|
|
248 235 <span class="k">my</span><span class="s">(</span><span class="i">$FirstBondLineIndex</span><span class="cm">,</span> <span class="i">$LastBondLineIndex</span><span class="cm">,</span> <span class="i">$FirstAtomNum</span><span class="cm">,</span> <span class="i">$SecondAtomNum</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="cm">,</span> <span class="i">$InternalBondOrder</span><span class="cm">,</span> <span class="i">$InternalBondType</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
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|
249 236
|
|
|
250 237 <span class="i">$FirstBondLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span><span class="sc">;</span>
|
|
|
251 238 <span class="i">$LastBondLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span> + <span class="i">$BondCount</span> - <span class="n">1</span><span class="sc">;</span>
|
|
|
252 239
|
|
|
253 240 <span class="k">for</span> <span class="s">(</span><span class="i">$LineIndex</span> = <span class="i">$FirstBondLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span> <= <span class="i">$LastBondLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span>++<span class="s">)</span> <span class="s">{</span>
|
|
|
254 241 <span class="s">(</span><span class="i">$FirstAtomNum</span><span class="cm">,</span> <span class="i">$SecondAtomNum</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdBondLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
255 242
|
|
|
256 243 <span class="i">$Atom1</span> = <span class="i">$AtomNumToAtomMap</span>{<span class="i">$FirstAtomNum</span>}<span class="sc">;</span>
|
|
|
257 244 <span class="i">$Atom2</span> = <span class="i">$AtomNumToAtomMap</span>{<span class="i">$SecondAtomNum</span>}<span class="sc">;</span>
|
|
|
258 245
|
|
|
259 246 <span class="s">(</span><span class="i">$InternalBondOrder</span><span class="cm">,</span> <span class="i">$InternalBondType</span><span class="s">)</span> = <span class="i">SDFileUtil::MDLBondTypeToInternalBondOrder</span><span class="s">(</span><span class="i">$BondType</span><span class="s">)</span><span class="sc">;</span>
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|
260 247 <span class="i">$Bond</span> = <span class="i">new</span> <span class="i">Bond</span><span class="s">(</span><span class="q">'Atoms'</span> <span class="cm">=></span> <span class="s">[</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">]</span><span class="cm">,</span> <span class="q">'BondOrder'</span> <span class="cm">=></span> <span class="i">$InternalBondOrder</span><span class="s">)</span><span class="sc">;</span>
|
|
|
261 248 <span class="i">$Bond</span><span class="i">->SetBondType</span><span class="s">(</span><span class="i">$InternalBondType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
262 249
|
|
|
263 250 <span class="k">if</span> <span class="s">(</span><span class="i">$BondStereo</span> && <span class="i">$BondStereo</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
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|
|
264 251 <span class="i">_ProcessBondStereo</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span><span class="sc">;</span>
|
|
|
265 252 <span class="s">}</span>
|
|
|
266 253
|
|
|
267 254 <span class="i">$Molecule</span><span class="i">->AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
268 255 <span class="s">}</span>
|
|
|
269 256
|
|
|
270 257 <span class="c"># Process available property block lines starting with A aaa, M CHG, M ISO and M RAD. All other property blocks</span>
|
|
|
271 258 <span class="c"># lines are for query or specific display purposes and are ignored for now.</span>
|
|
|
272 259 <span class="c">#</span>
|
|
|
273 260 <span class="c">#</span>
|
|
|
274 261 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyLineIndex</span><span class="cm">,</span> <span class="i">$PropertyLine</span><span class="cm">,</span> <span class="i">$FirstChargeOrRadicalLine</span><span class="cm">,</span> <span class="i">@ValuePairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
275 262
|
|
|
276 263 <span class="i">$PropertyLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span> + <span class="i">$BondCount</span><span class="sc">;</span>
|
|
|
277 264 <span class="i">$PropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span>
|
|
|
278 265 <span class="i">$FirstChargeOrRadicalLine</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
279 266
|
|
|
280 267 <span class="j">PROPERTYLINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$PropertyLine</span> !~ <span class="q">/^M END/i</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
281 268 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
282 269 <span class="k">last</span> <span class="j">PROPERTYLINE</span><span class="sc">;</span>
|
|
|
283 270 <span class="s">}</span>
|
|
|
284 271 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^(M CHG|M RAD)/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
285 272 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstChargeOrRadicalLine</span><span class="s">)</span> <span class="s">{</span>
|
|
|
286 273 <span class="i">$FirstChargeOrRadicalLine</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
287 274 <span class="i">_ZeroOutAtomsChargeAndRadicalValues</span><span class="s">(</span>\<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
288 275 <span class="s">}</span>
|
|
|
289 276 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M CHG/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
290 277 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdChargePropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
291 278 <span class="i">_ProcessChargeProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
292 279 <span class="s">}</span>
|
|
|
293 280 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M RAD/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
294 281 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdRadicalPropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
295 282 <span class="i">_ProcessRadicalProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
296 283 <span class="s">}</span>
|
|
|
297 284 <span class="s">}</span>
|
|
|
298 285 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M ISO/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
299 286 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdIsotopePropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
300 287 <span class="i">_ProcessIsotopeProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
301 288 <span class="s">}</span>
|
|
|
302 289 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^A /i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
303 290 <span class="k">my</span><span class="s">(</span><span class="i">$NextPropertyLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
304 291 <span class="i">$PropertyLineIndex</span>++<span class="sc">;</span>
|
|
|
305 292 <span class="i">$NextPropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span>
|
|
|
306 293 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdAtomAliasPropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="cm">,</span> <span class="i">$NextPropertyLine</span><span class="s">)</span><span class="sc">;</span>
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|
|
307 294 <span class="i">_ProcessAtomAliasProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
308 295 <span class="s">}</span>
|
|
|
309 296 <span class="i">$PropertyLineIndex</span>++<span class="sc">;</span>
|
|
|
310 297 <span class="i">$PropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span>
|
|
|
311 298 <span class="s">}</span>
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|
|
312 299 <span class="c"># Store input molecule string as generic property of molecule...</span>
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|
|
313 300 <span class="i">$Molecule</span><span class="i">->SetInputMoleculeString</span><span class="s">(</span><span class="i">$MoleculeString</span><span class="s">)</span><span class="sc">;</span>
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|
|
314 301
|
|
|
315 302 <span class="k">return</span> <span class="i">$Molecule</span><span class="sc">;</span>
|
|
|
316 303 <span class="s">}</span>
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|
|
317 304
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|
|
318 305 <span class="c"># Generate molecule string using molecule object...</span>
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|
319 <a name="GenerateMoleculeString-"></a> 306 <span class="k">sub </span><span class="m">GenerateMoleculeString</span> <span class="s">{</span>
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320 307 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
321 308 <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="sc">;</span>
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|
322 309
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|
323 310 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMDLMolFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
|
324 311 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
325 312 <span class="s">}</span>
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|
|
326 313 <span class="k">else</span> <span class="s">{</span>
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|
327 314 <span class="i">$Molecule</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
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|
|
328 315 <span class="i">$This</span> = <span class="k">undef</span><span class="sc">;</span>
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|
|
329 316 <span class="s">}</span>
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|
330 317 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
|
331 318 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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|
|
332 319 <span class="s">}</span>
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|
333 320 <span class="k">my</span><span class="s">(</span><span class="i">@MoleculeLines</span><span class="s">)</span><span class="sc">;</span>
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334 321 <span class="i">@MoleculeLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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335 322
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336 323 <span class="c"># First line: Molname line...</span>
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|
337 324 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdMolNameLine</span><span class="s">(</span><span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
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|
338 325
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|
339 326 <span class="c"># Second line: Misc info...</span>
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|
340 327 <span class="k">my</span><span class="s">(</span><span class="i">$ProgramName</span><span class="cm">,</span> <span class="i">$UserInitial</span><span class="cm">,</span> <span class="i">$Code</span><span class="s">)</span><span class="sc">;</span>
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|
|
341 328 <span class="i">$ProgramName</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$UserInitial</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$Code</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
342 329
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|
|
343 330 <span class="i">$Code</span> = <span class="i">$Molecule</span><span class="i">->IsThreeDimensional</span><span class="s">(</span><span class="s">)</span> ? <span class="q">'3D'</span> <span class="co">:</span> <span class="q">'2D'</span><span class="sc">;</span>
|
|
|
344 331
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|
345 332 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdMiscInfoLine</span><span class="s">(</span><span class="i">$ProgramName</span><span class="cm">,</span> <span class="i">$UserInitial</span><span class="cm">,</span> <span class="i">$Code</span><span class="s">)</span><span class="sc">;</span>
|
|
|
346 333
|
|
|
347 334 <span class="c"># Third line: Comments line...</span>
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|
|
348 335 <span class="k">my</span><span class="s">(</span><span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span>
|
|
|
349 336 <span class="i">$Comments</span> = <span class="i">$Molecule</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MDLComments'</span><span class="s">)</span> ? <span class="i">$Molecule</span><span class="i">->GetMDLComments</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Comments'</span><span class="s">)</span> ? <span class="i">$Molecule</span><span class="i">->GetComments</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span>
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|
350 337 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdCommentsLine</span><span class="s">(</span><span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span>
|
|
|
351 338
|
|
|
352 339 <span class="c"># Fourth line: Counts line for V2000</span>
|
|
|
353 340 <span class="k">my</span><span class="s">(</span><span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$BondCount</span><span class="cm">,</span> <span class="i">$ChiralFlag</span><span class="s">)</span><span class="sc">;</span>
|
|
|
354 341 <span class="i">$AtomCount</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
355 342 <span class="i">$BondCount</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
356 343 <span class="i">$ChiralFlag</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
357 344 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdCountsLine</span><span class="s">(</span><span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$BondCount</span><span class="cm">,</span> <span class="i">$ChiralFlag</span><span class="s">)</span><span class="sc">;</span>
|
|
|
358 345
|
|
|
359 346 <span class="c"># Atom lines...</span>
|
|
|
360 347 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">%AtomIDToNum</span><span class="s">)</span><span class="sc">;</span>
|
|
|
361 348 <span class="k">my</span><span class="s">(</span><span class="i">$ChargePropertyValue</span><span class="cm">,</span> <span class="i">$IsotopePropertyValue</span><span class="cm">,</span> <span class="i">$RadicalPropertyValue</span><span class="cm">,</span> <span class="i">$AtomAliasPropertyValue</span><span class="cm">,</span> <span class="i">@IsotopePropertyValuePairs</span><span class="cm">,</span> <span class="i">@ChargePropertyValuePairs</span><span class="cm">,</span> <span class="i">@RadicalPropertyValuePairs</span><span class="cm">,</span> <span class="i">@AtomAliasPropertyValuePairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
362 349
|
|
|
363 350 <span class="i">@ChargePropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
364 351 <span class="i">@IsotopePropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
365 352 <span class="i">@RadicalPropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
366 353 <span class="i">@AtomAliasPropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
367 354
|
|
|
368 355 <span class="i">@Atoms</span> = <span class="i">$Molecule</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
369 356
|
|
|
370 357 <span class="i">$AtomNum</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
371 358 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
372 359 <span class="i">$AtomNum</span>++<span class="sc">;</span>
|
|
|
373 360 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
374 361 <span class="i">$AtomIDToNum</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomNum</span><span class="sc">;</span>
|
|
|
375 362
|
|
|
376 363 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
377 364 <span class="s">(</span><span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="s">)</span> = <span class="i">$Atom</span><span class="i">->GetXYZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
378 365
|
|
|
379 366 <span class="c"># Setup mass difference...</span>
|
|
|
380 367 <span class="i">$MassDifference</span> = <span class="i">_GetMassDifference</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
381 368 <span class="k">if</span> <span class="s">(</span><span class="i">$MassDifference</span><span class="s">)</span> <span class="s">{</span>
|
|
|
382 369 <span class="c"># Hold it for M ISO property lines...</span>
|
|
|
383 370 <span class="i">$IsotopePropertyValue</span> = <span class="i">_GetIsotopePropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
384 371 <span class="k">if</span> <span class="s">(</span><span class="i">$IsotopePropertyValue</span><span class="s">)</span> <span class="s">{</span>
|
|
|
385 372 <span class="k">push</span> <span class="i">@IsotopePropertyValuePairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$IsotopePropertyValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
386 373 <span class="s">}</span>
|
|
|
387 374 <span class="s">}</span>
|
|
|
388 375
|
|
|
389 376 <span class="c"># Setup charge...</span>
|
|
|
390 377 <span class="i">$Charge</span> = <span class="i">_GetCharge</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
391 378 <span class="k">if</span> <span class="s">(</span><span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span>
|
|
|
392 379 <span class="c"># Hold it for M CHG property lines...</span>
|
|
|
393 380 <span class="i">$ChargePropertyValue</span> = <span class="i">_GetChargePropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
394 381 <span class="k">if</span> <span class="s">(</span><span class="i">$ChargePropertyValue</span><span class="s">)</span> <span class="s">{</span>
|
|
|
395 382 <span class="k">push</span> <span class="i">@ChargePropertyValuePairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$ChargePropertyValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
396 383 <span class="s">}</span>
|
|
|
397 384 <span class="s">}</span>
|
|
|
398 385
|
|
|
399 386 <span class="c"># Hold any radical values for for M RAD property lines...</span>
|
|
|
400 387 <span class="i">$RadicalPropertyValue</span> = <span class="i">_GetRadicalPropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
401 388 <span class="k">if</span> <span class="s">(</span><span class="i">$RadicalPropertyValue</span><span class="s">)</span> <span class="s">{</span>
|
|
|
402 389 <span class="k">push</span> <span class="i">@RadicalPropertyValuePairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$RadicalPropertyValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
403 390 <span class="s">}</span>
|
|
|
404 391
|
|
|
405 392 <span class="c"># Hold any atom alias value for A xxx property lines....</span>
|
|
|
406 393 <span class="i">$AtomAliasPropertyValue</span> = <span class="i">_GetAtomAliasPropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
407 394 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomAliasPropertyValue</span><span class="s">)</span> <span class="s">{</span>
|
|
|
408 395 <span class="k">push</span> <span class="i">@AtomAliasPropertyValuePairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$AtomAliasPropertyValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
409 396
|
|
|
410 397 <span class="c"># Set AtomSymbol to carbon as atom alias would override its value during parsing...</span>
|
|
|
411 398 <span class="i">$AtomSymbol</span> = <span class="q">"C"</span><span class="sc">;</span>
|
|
|
412 399 <span class="s">}</span>
|
|
|
413 400
|
|
|
414 401 <span class="c"># Setup stereo parity...</span>
|
|
|
415 402 <span class="i">$StereoParity</span> = <span class="i">_GetStereoParity</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
416 403
|
|
|
417 404 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdAtomLine</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
418 405 <span class="s">}</span>
|
|
|
419 406
|
|
|
420 407 <span class="c"># Bond lines...</span>
|
|
|
421 408 <span class="k">my</span><span class="s">(</span><span class="i">$FirstAtomID</span><span class="cm">,</span> <span class="i">$FirstAtom</span><span class="cm">,</span> <span class="i">$FirstAtomNum</span><span class="cm">,</span> <span class="i">$SecondAtomID</span><span class="cm">,</span> <span class="i">$SecondAtom</span><span class="cm">,</span> <span class="i">$SecondAtomNum</span><span class="cm">,</span> <span class="i">$MDLBondType</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$MDLBondStereo</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
422 409 <span class="k">for</span> <span class="i">$FirstAtom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
423 410 <span class="i">$FirstAtomID</span> = <span class="i">$FirstAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
424 411 <span class="i">$FirstAtomNum</span> = <span class="i">$AtomIDToNum</span>{<span class="i">$FirstAtomID</span>}<span class="sc">;</span>
|
|
|
425 412
|
|
|
426 413 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
427 414 <span class="i">@Bonds</span> = <span class="i">$FirstAtom</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
428 415 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
429 416 <span class="i">$SecondAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$FirstAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
430 417 <span class="i">$SecondAtomID</span> = <span class="i">$SecondAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
431 418 <span class="i">$SecondAtomNum</span> = <span class="i">$AtomIDToNum</span>{<span class="i">$SecondAtomID</span>}<span class="sc">;</span>
|
|
|
432 419 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomNum</span> >= <span class="i">$SecondAtomNum</span><span class="s">)</span> <span class="s">{</span>
|
|
|
433 420 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
434 421 <span class="s">}</span>
|
|
|
435 422 <span class="c"># Setup BondType...</span>
|
|
|
436 423 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
437 424 <span class="i">$BondType</span> = <span class="i">$Bond</span><span class="i">->GetBondType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
438 425 <span class="i">$MDLBondType</span> = <span class="i">SDFileUtil::InternalBondOrderToMDLBondType</span><span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$BondType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
439 426
|
|
|
440 427 <span class="c"># Setup BondStereo...</span>
|
|
|
441 428 <span class="i">$MDLBondStereo</span> = <span class="i">_GetBondStereo</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
442 429
|
|
|
443 430 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdBondLine</span><span class="s">(</span><span class="i">$FirstAtomNum</span><span class="cm">,</span> <span class="i">$SecondAtomNum</span><span class="cm">,</span> <span class="i">$MDLBondType</span><span class="cm">,</span> <span class="i">$MDLBondStereo</span><span class="s">)</span><span class="sc">;</span>
|
|
|
444 431 <span class="s">}</span>
|
|
|
445 432 <span class="s">}</span>
|
|
|
446 433 <span class="c"># Property lines...</span>
|
|
|
447 434 <span class="k">if</span> <span class="s">(</span><span class="i">@IsotopePropertyValuePairs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
448 435 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdIsotopePropertyLines</span><span class="s">(</span>\<span class="i">@IsotopePropertyValuePairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
449 436 <span class="s">}</span>
|
|
|
450 437 <span class="k">if</span> <span class="s">(</span><span class="i">@ChargePropertyValuePairs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
451 438 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdChargePropertyLines</span><span class="s">(</span>\<span class="i">@ChargePropertyValuePairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
452 439 <span class="s">}</span>
|
|
|
453 440 <span class="k">if</span> <span class="s">(</span><span class="i">@RadicalPropertyValuePairs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
454 441 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdRadicalPropertyLines</span><span class="s">(</span>\<span class="i">@RadicalPropertyValuePairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
455 442 <span class="s">}</span>
|
|
|
456 443 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomAliasPropertyValuePairs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
457 444 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdAtomAliasPropertyLines</span><span class="s">(</span>\<span class="i">@AtomAliasPropertyValuePairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
458 445 <span class="s">}</span>
|
|
|
459 446
|
|
|
460 447 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="q">"M END"</span><span class="sc">;</span>
|
|
|
461 448
|
|
|
462 449 <span class="k">return</span> <span class="k">join</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">@MoleculeLines</span><span class="sc">;</span>
|
|
|
463 450 <span class="s">}</span>
|
|
|
464 451
|
|
|
465 452 <span class="c"># Process MassDifference value and set atom's mass number...</span>
|
|
|
466 453 <span class="c">#</span>
|
|
|
467 <a name="_ProcessMassDifference-"></a> 454 <span class="k">sub </span><span class="m">_ProcessMassDifference</span> <span class="s">{</span>
|
|
|
468 455 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
469 456 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="cm">,</span> <span class="i">$NewMassNumber</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
470 457
|
|
|
471 458 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
472 459
|
|
|
473 460 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
474 461 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessMassDifference: Ignoring specified mass difference value, $MassDifference, in SD file: Assigned to non standard element..."</span><span class="sc">;</span>
|
|
|
475 462 <span class="k">return</span><span class="sc">;</span>
|
|
|
476 463 <span class="s">}</span>
|
|
|
477 464 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
478 465 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MassDifference</span><span class="s">)</span> <span class="s">{</span>
|
|
|
479 466 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessMassDifference: Ignoring specified mass difference value, $MassDifference, in SD file: Unknown MassNumber value..."</span><span class="sc">;</span>
|
|
|
480 467 <span class="k">return</span><span class="sc">;</span>
|
|
|
481 468 <span class="s">}</span>
|
|
|
482 469 <span class="i">$NewMassNumber</span> = <span class="i">$MassNumber</span> + <span class="i">$MassDifference</span><span class="sc">;</span>
|
|
|
483 470 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$NewMassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
484 471 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
485 472 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessMassDifference: Unknown mass number, $MassNumber, corresponding to specified mass difference value, $MassDifference, in SD for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. The mass number value has been assigned. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...\n"</span><span class="sc">;</span>
|
|
|
486 473 <span class="s">}</span>
|
|
|
487 474
|
|
|
488 475 <span class="c"># Use SetProperty method instead of SetMassNumber to skip explicit checks on MassNumber value...</span>
|
|
|
489 476 <span class="i">$Atom</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="cm">,</span> <span class="i">$NewMassNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
490 477 <span class="s">}</span>
|
|
|
491 478
|
|
|
492 479 <span class="c"># Get mass difference value...</span>
|
|
|
493 <a name="_GetMassDifference-"></a> 480 <span class="k">sub </span><span class="m">_GetMassDifference</span> <span class="s">{</span>
|
|
|
494 481 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
495 482 <span class="k">my</span><span class="s">(</span><span class="i">$MassDifference</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="cm">,</span> <span class="i">$MostAbundantMassNumber</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
496 483
|
|
|
497 484 <span class="i">$MassDifference</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
498 485 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
499 486 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$MassNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
500 487 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
501 488 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
502 489 <span class="i">$MostAbundantMassNumber</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
503 490 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$MostAbundantMassNumber</span><span class="s">)</span> && <span class="i">$MassNumber</span> != <span class="i">$MostAbundantMassNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
504 491 <span class="i">$MassDifference</span> = <span class="i">$MassNumber</span> - <span class="i">$MostAbundantMassNumber</span><span class="sc">;</span>
|
|
|
505 492 <span class="s">}</span>
|
|
|
506 493 <span class="s">}</span>
|
|
|
507 494 <span class="s">}</span>
|
|
|
508 495 <span class="k">return</span> <span class="i">$MassDifference</span><span class="sc">;</span>
|
|
|
509 496 <span class="s">}</span>
|
|
|
510 497
|
|
|
511 498 <span class="c"># Process formal charge value and assign it to atom as formal charge...</span>
|
|
|
512 <a name="_ProcessCharge-"></a> 499 <span class="k">sub </span><span class="m">_ProcessCharge</span> <span class="s">{</span>
|
|
|
513 500 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$Charge</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
514 501 <span class="k">my</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
515 502
|
|
|
516 503 <span class="i">$InternalCharge</span> = <span class="i">SDFileUtil::MDLChargeToInternalCharge</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
517 504 <span class="i">$Atom</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
518 505 <span class="s">}</span>
|
|
|
519 506
|
|
|
520 507 <span class="c"># Get MDL formal charge value ...</span>
|
|
|
521 <a name="_GetCharge-"></a> 508 <span class="k">sub </span><span class="m">_GetCharge</span> <span class="s">{</span>
|
|
|
522 509 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
523 510 <span class="k">my</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="cm">,</span> <span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
524 511
|
|
|
525 512 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
526 513 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
527 514 <span class="i">$InternalCharge</span> = <span class="i">$Atom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
528 515 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span> <span class="s">{</span>
|
|
|
529 516 <span class="i">$Charge</span> = <span class="i">SDFileUtil::InternalChargeToMDLCharge</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
530 517 <span class="s">}</span>
|
|
|
531 518 <span class="s">}</span>
|
|
|
532 519 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span>
|
|
|
533 520 <span class="s">}</span>
|
|
|
534 521
|
|
|
535 522 <span class="c"># Process stereo parity value and assign it to atom as MDL property...</span>
|
|
|
536 523 <span class="c">#</span>
|
|
|
537 524 <span class="c"># Notes:</span>
|
|
|
538 525 <span class="c"># . Mark atom as chiral center</span>
|
|
|
539 526 <span class="c"># . Assign any explicit Clockwise (parity 1), CounterClockwise (parity 2) or either value (parity 3) as property of atom.</span>
|
|
|
540 527 <span class="c"># . MDL values of Clockwise and CounterClockwise don't correspond to priority assigned to ligands around</span>
|
|
|
541 528 <span class="c"># stereo center using CIP scheme; consequently, these values can't be used to set internal Stereochemistry for</span>
|
|
|
542 529 <span class="c"># an atom.</span>
|
|
|
543 530 <span class="c">#</span>
|
|
|
544 <a name="_ProcessStereoParity-"></a> 531 <span class="k">sub </span><span class="m">_ProcessStereoParity</span> <span class="s">{</span>
|
|
|
545 532 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
546 533
|
|
|
547 534 <span class="i">$Atom</span><span class="i">->SetStereoCenter</span><span class="s">(</span><span class="q">'1'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
548 535 <span class="i">$Atom</span><span class="i">->SetMDLStereoParity</span><span class="s">(</span><span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
549 536 <span class="s">}</span>
|
|
|
550 537
|
|
|
551 538 <span class="c"># Set stereo parity value to zero for now: The current release of MayaChemTools hasn't implemented</span>
|
|
|
552 539 <span class="c"># functionality to determine chirality.</span>
|
|
|
553 540 <span class="c">#</span>
|
|
|
554 <a name="_GetStereoParity-"></a> 541 <span class="k">sub </span><span class="m">_GetStereoParity</span> <span class="s">{</span>
|
|
|
555 542 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
556 543 <span class="k">my</span><span class="s">(</span><span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
557 544
|
|
|
558 545 <span class="i">$StereoParity</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
559 546
|
|
|
560 547 <span class="k">return</span> <span class="i">$StereoParity</span><span class="sc">;</span>
|
|
|
561 548 <span class="s">}</span>
|
|
|
562 549
|
|
|
563 550 <span class="c"># Process bond stereo value...</span>
|
|
|
564 <a name="_ProcessBondStereo-"></a> 551 <span class="k">sub </span><span class="m">_ProcessBondStereo</span> <span class="s">{</span>
|
|
|
565 552 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
566 553 <span class="k">my</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span><span class="sc">;</span>
|
|
|
567 554
|
|
|
568 555 <span class="i">$InternalBondStereo</span> = <span class="i">SDFileUtil::MDLBondStereoToInternalBondStereochemistry</span><span class="s">(</span><span class="i">$BondStereo</span><span class="s">)</span><span class="sc">;</span>
|
|
|
569 556 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span> <span class="s">{</span>
|
|
|
570 557 <span class="i">$Bond</span><span class="i">->SetBondStereochemistry</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span><span class="sc">;</span>
|
|
|
571 558 <span class="s">}</span>
|
|
|
572 559 <span class="s">}</span>
|
|
|
573 560
|
|
|
574 561 <span class="c"># Get MDLBondStereo value...</span>
|
|
|
575 <a name="_GetBondStereo-"></a> 562 <span class="k">sub </span><span class="m">_GetBondStereo</span> <span class="s">{</span>
|
|
|
576 563 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
577 564 <span class="k">my</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span><span class="sc">;</span>
|
|
|
578 565
|
|
|
579 566 <span class="i">$BondStereo</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
580 567
|
|
|
581 568 <span class="i">$InternalBondStereo</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
582 569 <span class="j">BONDSTEREO:</span> <span class="s">{</span>
|
|
|
583 570 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsUp</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
584 571 <span class="i">$InternalBondStereo</span> = <span class="q">'Up'</span><span class="sc">;</span>
|
|
|
585 572 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span>
|
|
|
586 573 <span class="s">}</span>
|
|
|
587 574 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsDown</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
588 575 <span class="i">$InternalBondStereo</span> = <span class="q">'Down'</span><span class="sc">;</span>
|
|
|
589 576 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span>
|
|
|
590 577 <span class="s">}</span>
|
|
|
591 578 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsUpOrDown</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
592 579 <span class="i">$InternalBondStereo</span> = <span class="q">'UpOrDown'</span><span class="sc">;</span>
|
|
|
593 580 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span>
|
|
|
594 581 <span class="s">}</span>
|
|
|
595 582 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsCisOrTrans</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">->IsCis</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">->IsTrans</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
596 583 <span class="i">$InternalBondStereo</span> = <span class="q">'CisOrTrans'</span><span class="sc">;</span>
|
|
|
597 584 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span>
|
|
|
598 585 <span class="s">}</span>
|
|
|
599 586 <span class="i">$InternalBondStereo</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
600 587 <span class="s">}</span>
|
|
|
601 588
|
|
|
602 589 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span> <span class="s">{</span>
|
|
|
603 590 <span class="i">$BondStereo</span> = <span class="i">SDFileUtil::InternalBondStereochemistryToMDLBondStereo</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span><span class="sc">;</span>
|
|
|
604 591 <span class="s">}</span>
|
|
|
605 592
|
|
|
606 593 <span class="k">return</span> <span class="i">$BondStereo</span><span class="sc">;</span>
|
|
|
607 594 <span class="s">}</span>
|
|
|
608 595
|
|
|
609 596 <span class="c"># Zero out charge and radical values specified for atoms...</span>
|
|
|
610 <a name="_ZeroOutAtomsChargeAndRadicalValues-"></a> 597 <span class="k">sub </span><span class="m">_ZeroOutAtomsChargeAndRadicalValues</span> <span class="s">{</span>
|
|
|
611 598 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
612 599 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
613 600
|
|
|
614 601 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="k">values</span> <span class="i">%</span>{<span class="i">$AtomNumToAtomMapRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
615 602 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
616 603 <span class="i">$Atom</span><span class="i">->DeleteProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
617 604 <span class="s">}</span>
|
|
|
618 605 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom</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>
|
|
|
619 606 <span class="i">$Atom</span><span class="i">->DeleteProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
620 607 <span class="s">}</span>
|
|
|
621 608 <span class="s">}</span>
|
|
|
622 609 <span class="s">}</span>
|
|
|
623 610
|
|
|
624 611 <span class="c"># Process charge property value pairs...</span>
|
|
|
625 <a name="_ProcessChargeProperty-"></a> 612 <span class="k">sub </span><span class="m">_ProcessChargeProperty</span> <span class="s">{</span>
|
|
|
626 613 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
627 614
|
|
|
628 615 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
629 616 <span class="k">return</span><span class="sc">;</span>
|
|
|
630 617 <span class="s">}</span>
|
|
|
631 618 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ValuePairsCount</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
632 619
|
|
|
633 620 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span>
|
|
|
634 621 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
635 622 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$Charge</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
636 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span>
|
|
|
637 624 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
|
|
|
638 625 <span class="s">}</span>
|
|
|
639 626 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
640 627 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
|
|
|
641 628 <span class="s">}</span>
|
|
|
642 629 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span>
|
|
|
643 630 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
644 631 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessChargeProperty: Setting formal charge on atom number, $AtomNum, with already assigned spin multiplicity value..."</span><span class="sc">;</span>
|
|
|
645 632 <span class="s">}</span>
|
|
|
646 633 <span class="i">$Atom</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
647 634 <span class="s">}</span>
|
|
|
648 635 <span class="s">}</span>
|
|
|
649 636
|
|
|
650 637 <span class="c"># Get charge property value for an atom...</span>
|
|
|
651 <a name="_GetChargePropertyValue-"></a> 638 <span class="k">sub </span><span class="m">_GetChargePropertyValue</span> <span class="s">{</span>
|
|
|
652 639 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
653 640 <span class="k">my</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
654 641
|
|
|
655 642 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
656 643 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
657 644 <span class="i">$Charge</span> = <span class="i">$Atom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
658 645 <span class="s">}</span>
|
|
|
659 646 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span>
|
|
|
660 647 <span class="s">}</span>
|
|
|
661 648
|
|
|
662 649 <span class="c"># Process charge property value pairs...</span>
|
|
|
663 <a name="_ProcessRadicalProperty-"></a> 650 <span class="k">sub </span><span class="m">_ProcessRadicalProperty</span> <span class="s">{</span>
|
|
|
664 651 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
665 652
|
|
|
666 653 <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">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
667 654 <span class="k">return</span><span class="sc">;</span>
|
|
|
668 655 <span class="s">}</span>
|
|
|
669 656 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ValuePairsCount</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$Radical</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
670 657
|
|
|
671 658 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span>
|
|
|
672 659 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
673 660 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$Radical</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
674 661 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Radical</span><span class="s">)</span> <span class="s">{</span>
|
|
|
675 662 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
|
|
|
676 663 <span class="s">}</span>
|
|
|
677 664 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
678 665 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
|
|
|
679 666 <span class="s">}</span>
|
|
|
680 667 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span>
|
|
|
681 668 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
682 669 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessRadicalProperty: Setting spin multiplicity on atom number, $AtomNum, with already assigned formal charge value..."</span><span class="sc">;</span>
|
|
|
683 670 <span class="s">}</span>
|
|
|
684 671 <span class="i">$SpinMultiplicity</span> = <span class="i">SDFileUtil::MDLRadicalToInternalSpinMultiplicity</span><span class="s">(</span><span class="i">$Radical</span><span class="s">)</span><span class="sc">;</span>
|
|
|
685 672 <span class="i">$Atom</span><span class="i">->SetSpinMultiplicity</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
686 673 <span class="s">}</span>
|
|
|
687 674 <span class="s">}</span>
|
|
|
688 675
|
|
|
689 676 <span class="c"># Get radical property value for an atom...</span>
|
|
|
690 <a name="_GetRadicalPropertyValue-"></a> 677 <span class="k">sub </span><span class="m">_GetRadicalPropertyValue</span> <span class="s">{</span>
|
|
|
691 678 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
692 679 <span class="k">my</span><span class="s">(</span><span class="i">$Radical</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
693 680
|
|
|
694 681 <span class="i">$Radical</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
695 682 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
696 683 <span class="i">$SpinMultiplicity</span> = <span class="i">$Atom</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
697 684 <span class="i">$Radical</span> = <span class="i">SDFileUtil::InternalSpinMultiplicityToMDLRadical</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
698 685 <span class="s">}</span>
|
|
|
699 686 <span class="k">return</span> <span class="i">$Radical</span><span class="sc">;</span>
|
|
|
700 687 <span class="s">}</span>
|
|
|
701 688
|
|
|
702 689 <span class="c"># Process isotope property value pairs...</span>
|
|
|
703 <a name="_ProcessIsotopeProperty-"></a> 690 <span class="k">sub </span><span class="m">_ProcessIsotopeProperty</span> <span class="s">{</span>
|
|
|
704 691 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
705 692
|
|
|
706 693 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
707 694 <span class="k">return</span><span class="sc">;</span>
|
|
|
708 695 <span class="s">}</span>
|
|
|
709 696 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ValuePairsCount</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
710 697
|
|
|
711 698 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span>
|
|
|
712 699 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
713 700 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$MassNumber</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
714 701 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MassNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
715 702 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
|
|
|
716 703 <span class="s">}</span>
|
|
|
717 704 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
718 705 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
|
|
|
719 706 <span class="s">}</span>
|
|
|
720 707 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span>
|
|
|
721 708 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
722 709
|
|
|
723 710 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
724 711 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
725 712 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessProcessIsotopeProperty: Unknown mass number, $MassNumber, specified on M ISO property line for atom number, $AtomNum, in SD for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. The mass number value has been assigned. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...\n"</span><span class="sc">;</span>
|
|
|
726 713 <span class="s">}</span>
|
|
|
727 714
|
|
|
728 715 <span class="c"># Use SetProperty method instead of SetMassNumber to skip explicit checks on MassNumber value...</span>
|
|
|
729 716 <span class="i">$Atom</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
730 717 <span class="s">}</span>
|
|
|
731 718 <span class="s">}</span>
|
|
|
732 719
|
|
|
733 720 <span class="c"># Get isotope property value for an atom...</span>
|
|
|
734 <a name="_GetIsotopePropertyValue-"></a> 721 <span class="k">sub </span><span class="m">_GetIsotopePropertyValue</span> <span class="s">{</span>
|
|
|
735 722 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
736 723 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
737 724
|
|
|
738 725 <span class="i">$MassNumber</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
739 726 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
740 727 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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741 728 <span class="s">}</span>
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742 729 <span class="k">return</span> <span class="i">$MassNumber</span><span class="sc">;</span>
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|
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743 730 <span class="s">}</span>
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744 731
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745 732 <span class="c"># Process atom alias property value pairs...</span>
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|
|
746 <a name="_ProcessAtomAliasProperty-"></a> 733 <span class="k">sub </span><span class="m">_ProcessAtomAliasProperty</span> <span class="s">{</span>
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|
|
747 734 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
|
748 735
|
|
|
749 736 <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">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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750 737 <span class="k">return</span><span class="sc">;</span>
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|
751 738 <span class="s">}</span>
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|
752 739 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ValuePairsCount</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$AtomAlias</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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|
|
753 740
|
|
|
754 741 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span>
|
|
|
755 742 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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|
756 743 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$AtomAlias</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
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|
|
757 744 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomNum</span><span class="s">)</span> <span class="s">{</span>
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758 745 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
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|
|
759 746 <span class="s">}</span>
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|
|
760 747 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
761 748 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
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|
|
762 749 <span class="s">}</span>
|
|
|
763 750 <span class="i">$AtomAlias</span> = <span class="i">TextUtil::RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span>
|
|
|
764 751 <span class="k">if</span> <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
765 752 <span class="i">carp</span><span class="s">(</span><span class="q">"Warning: ${ClassName}->_ProcessAtomAliasProperty: Ignoring atom alias property line: No Atom alias value specified..."</span><span class="s">)</span><span class="sc">;</span>
|
|
|
766 753 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
|
|
|
767 754 <span class="s">}</span>
|
|
|
768 755
|
|
|
769 756 <span class="c"># Set atom symbol to atom alias which sets atomic number automatically...</span>
|
|
|
770 757 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span>
|
|
|
771 758 <span class="i">$Atom</span><span class="i">->SetAtomSymbol</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span>
|
|
|
772 759
|
|
|
773 760 <span class="i">$Atom</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'AtomAlias'</span><span class="cm">,</span> <span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span>
|
|
|
774 761 <span class="s">}</span>
|
|
|
775 762 <span class="s">}</span>
|
|
|
776 763
|
|
|
777 764 <span class="c"># Get atom alias property value for an atom...</span>
|
|
|
778 <a name="_GetAtomAliasPropertyValue-"></a> 765 <span class="k">sub </span><span class="m">_GetAtomAliasPropertyValue</span> <span class="s">{</span>
|
|
|
779 766 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
780 767 <span class="k">my</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span>
|
|
|
781 768
|
|
|
782 769 <span class="i">$AtomAlias</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
783 770 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'AtomAlias'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
784 771 <span class="i">$AtomAlias</span> = <span class="i">$Atom</span><span class="i">->GetAtomAlias</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
785 772 <span class="s">}</span>
|
|
|
786 773 <span class="k">return</span> <span class="i">$AtomAlias</span><span class="sc">;</span>
|
|
|
787 774 <span class="s">}</span>
|
|
|
788 775
|
|
|
789 776 <span class="c"># Is it a MDLMolFileIO object?</span>
|
|
|
790 <a name="_IsMDLMolFileIO-"></a> 777 <span class="k">sub </span><span class="m">_IsMDLMolFileIO</span> <span class="s">{</span>
|
|
|
791 778 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
792 779
|
|
|
793 780 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
794 781 <span class="s">}</span>
|
|
|
795 782
|
|
|
796 783
|
|
|
797 <a name="EOF-"></a></pre>
|
|
|
798 <p> </p>
|
|
|
799 <br />
|
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|
800 <center>
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|
801 <img src="../../../images/h2o2.png">
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|
802 </center>
|
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803 </body>
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804 </html>
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