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1 <html>
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2 <head>
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3 <title>MayaChemTools:Code:FileIO::MDLMolFileIO.pm</title>
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4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
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5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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6 </head>
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7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
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8 <br/>
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9 <center>
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10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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11 </center>
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12 <br/>
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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 &lt;msud@san.rr.com&gt;</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 &lt;http://www.gnu.org/licenses/&gt; 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">=&gt;</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">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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70 57 <span class="k">bless</span> <span class="i">$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">$This</span><span class="i">-&gt;_InitializeMDLMolFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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72 59
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73 60 <span class="i">$This</span><span class="i">-&gt;_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">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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98 85
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99 86 <span class="c"># All other property names and values along with all Set/Get&lt;PropertyName&gt; methods</span>
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100 87 <span class="c"># are implemented on-demand using ObjectProperty class.</span>
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101 88
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102 89 <span class="k">my</span><span class="s">(</span><span class="i">$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">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
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105 92 <span class="i">$This</span><span class="i">-&gt;$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">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying file name...&quot;</span><span class="sc">;</span>
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110 97 <span class="s">}</span>
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111 98
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112 99 <span class="c"># Make sure it&#39;s a MDLMol file...</span>
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113 100 <span class="i">$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">-&gt;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">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated: File, $Name, doesn&#39;t appear to be MDLMol format...&quot;</span><span class="sc">;</span>
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116 103 <span class="s">}</span>
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117 104
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118 105 <span class="k">return</span> <span class="i">$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">$Status</span><span class="s">)</span><span class="sc">;</span>
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125 112
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126 113 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">_IsMDLMolFileIO</span><span class="s">(</span><span class="i">$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">&quot;mol&quot;</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">$This</span><span class="i">-&gt;GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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145 132 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;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> &amp;&amp; <span class="i">$Molecule</span><span class="i">-&gt;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">&quot;Warning: ${ClassName}-&gt;WriteMolecule: No data written: Molecule object is not specified...&quot;</span><span class="sc">;</span>
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154 141 <span class="k">return</span> <span class="i">$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">$This</span><span class="i">-&gt;GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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158 145
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159 146 <span class="k">print</span> <span class="i">$FileHandle</span> <span class="i">$This</span><span class="i">-&gt;GenerateMoleculeString</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> . <span class="q">&quot;\n&quot;</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">$This</span><span class="i">-&gt;GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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170 157 <span class="k">return</span> <span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$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> &amp;&amp; <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">-&gt;SetValenceModel</span><span class="s">(</span><span class="q">&#39;MDLValenceModel&#39;</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">$Molecule</span><span class="i">-&gt;SetName</span><span class="s">(</span><span class="i">$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">-&gt;SetProperties</span><span class="s">(</span><span class="q">&#39;MDLUserInitial&#39;</span> <span class="cm">=&gt;</span> <span class="i">$UserInitial</span><span class="cm">,</span> <span class="q">&#39;MDLProgramName&#39;</span> <span class="cm">=&gt;</span> <span class="i">$ProgramName</span><span class="cm">,</span> <span class="q">&#39;MDLDate&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Date</span><span class="cm">,</span> <span class="q">&#39;MDLCode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Code</span><span class="cm">,</span> <span class="q">&#39;MDLScalingFactor1&#39;</span> <span class="cm">=&gt;</span> <span class="i">$ScalingFactor1</span><span class="cm">,</span> <span class="q">&#39;MDLScalingFactor2&#39;</span> <span class="cm">=&gt;</span> <span class="i">$ScalingFactor2</span><span class="cm">,</span> <span class="q">&#39;MDLEnergy&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Energy</span><span class="cm">,</span> <span class="q">&#39;MDLRegistryNum&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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">$Molecule</span><span class="i">-&gt;SetProperties</span><span class="s">(</span><span class="q">&#39;MDLComments&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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">$Molecule</span><span class="i">-&gt;SetProperties</span><span class="s">(</span><span class="q">&#39;MDLChiralFlag&#39;</span> <span class="cm">=&gt;</span> <span class="i">$ChiralFlag</span><span class="cm">,</span> <span class="q">&#39;MDLPropertyCount&#39;</span> <span class="cm">=&gt;</span> <span class="i">$PropertyCount</span><span class="cm">,</span> <span class="q">&#39;MDLVersion&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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">$Atom</span><span class="cm">,</span> <span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
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222 209
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223 210 <span class="i">$AtomNum</span> = <span class="n">0</span><span class="sc">;</span>
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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
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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">$LineIndex</span> &lt;= <span class="i">$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>
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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">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span>
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230 217
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231 218 <span class="i">$Atom</span> = <span class="i">new</span> <span class="i">Atom</span><span class="s">(</span><span class="q">&#39;AtomSymbol&#39;</span> <span class="cm">=&gt;</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="q">&#39;XYZ&#39;</span> <span class="cm">=&gt;</span> <span class="s">[</span><span class="i">$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
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233 220 <span class="k">if</span> <span class="s">(</span><span class="i">$MassDifference</span> &amp;&amp; <span class="i">$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>
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235 222 <span class="s">}</span>
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236 223 <span class="k">if</span> <span class="s">(</span><span class="i">$Charge</span> &amp;&amp; <span class="i">$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>
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238 225 <span class="s">}</span>
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239 226 <span class="k">if</span> <span class="s">(</span><span class="i">$StereoParity</span> &amp;&amp; <span class="i">$StereoParity</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
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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>
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241 228 <span class="s">}</span>
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242 229
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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">-&gt;AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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245 232 <span class="s">}</span>
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246 233
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247 234 <span class="c"># Process bond data...</span>
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248 235 <span class="k">my</span><span class="s">(</span><span class="i">$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
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250 237 <span class="i">$FirstBondLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span><span class="sc">;</span>
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251 238 <span class="i">$LastBondLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span> + <span class="i">$BondCount</span> - <span class="n">1</span><span class="sc">;</span>
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252 239
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253 240 <span class="k">for</span> <span class="s">(</span><span class="i">$LineIndex</span> = <span class="i">$FirstBondLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span> &lt;= <span class="i">$LastBondLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span>++<span class="s">)</span> <span class="s">{</span>
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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>
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255 242
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256 243 <span class="i">$Atom1</span> = <span class="i">$AtomNumToAtomMap</span>{<span class="i">$FirstAtomNum</span>}<span class="sc">;</span>
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257 244 <span class="i">$Atom2</span> = <span class="i">$AtomNumToAtomMap</span>{<span class="i">$SecondAtomNum</span>}<span class="sc">;</span>
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258 245
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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">&#39;Atoms&#39;</span> <span class="cm">=&gt;</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">&#39;BondOrder&#39;</span> <span class="cm">=&gt;</span> <span class="i">$InternalBondOrder</span><span class="s">)</span><span class="sc">;</span>
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261 248 <span class="i">$Bond</span><span class="i">-&gt;SetBondType</span><span class="s">(</span><span class="i">$InternalBondType</span><span class="s">)</span><span class="sc">;</span>
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262 249
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263 250 <span class="k">if</span> <span class="s">(</span><span class="i">$BondStereo</span> &amp;&amp; <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">$BondStereo</span><span class="s">)</span><span class="sc">;</span>
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265 252 <span class="s">}</span>
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266 253
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267 254 <span class="i">$Molecule</span><span class="i">-&gt;AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
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268 255 <span class="s">}</span>
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269 256
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270 257 <span class="c"># Process available property block lines starting with A aaa, M CHG, M ISO and M RAD. All other property blocks</span>
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271 258 <span class="c"># lines are for query or specific display purposes and are ignored for now.</span>
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272 259 <span class="c">#</span>
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273 260 <span class="c">#</span>
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274 261 <span class="k">my</span><span class="s">(</span><span class="i">$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>
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275 262
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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>
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277 264 <span class="i">$PropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span>
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278 265 <span class="i">$FirstChargeOrRadicalLine</span> = <span class="n">1</span><span class="sc">;</span>
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279 266
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280 267 <span class="j">PROPERTYLINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$PropertyLine</span> !~ <span class="q">/^M END/i</span> <span class="s">)</span> <span class="s">{</span>
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281 268 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span>
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282 269 <span class="k">last</span> <span class="j">PROPERTYLINE</span><span class="sc">;</span>
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283 270 <span class="s">}</span>
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284 271 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^(M CHG|M RAD)/i</span><span class="s">)</span> <span class="s">{</span>
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285 272 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstChargeOrRadicalLine</span><span class="s">)</span> <span class="s">{</span>
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286 273 <span class="i">$FirstChargeOrRadicalLine</span> = <span class="n">0</span><span class="sc">;</span>
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287 274 <span class="i">_ZeroOutAtomsChargeAndRadicalValues</span><span class="s">(</span>\<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
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288 275 <span class="s">}</span>
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289 276 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M CHG/i</span><span class="s">)</span> <span class="s">{</span>
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290 277 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdChargePropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span>
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291 278 <span class="i">_ProcessChargeProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
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292 279 <span class="s">}</span>
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293 280 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M RAD/i</span><span class="s">)</span> <span class="s">{</span>
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294 281 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdRadicalPropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span>
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295 282 <span class="i">_ProcessRadicalProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
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296 283 <span class="s">}</span>
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297 284 <span class="s">}</span>
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298 285 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M ISO/i</span><span class="s">)</span> <span class="s">{</span>
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299 286 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdIsotopePropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span>
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300 287 <span class="i">_ProcessIsotopeProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
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301 288 <span class="s">}</span>
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302 289 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^A /i</span><span class="s">)</span> <span class="s">{</span>
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303 290 <span class="k">my</span><span class="s">(</span><span class="i">$NextPropertyLine</span><span class="s">)</span><span class="sc">;</span>
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304 291 <span class="i">$PropertyLineIndex</span>++<span class="sc">;</span>
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305 292 <span class="i">$NextPropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span>
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306 293 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdAtomAliasPropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="cm">,</span> <span class="i">$NextPropertyLine</span><span class="s">)</span><span class="sc">;</span>
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307 294 <span class="i">_ProcessAtomAliasProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span>
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308 295 <span class="s">}</span>
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309 296 <span class="i">$PropertyLineIndex</span>++<span class="sc">;</span>
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310 297 <span class="i">$PropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span>
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311 298 <span class="s">}</span>
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312 299 <span class="c"># Store input molecule string as generic property of molecule...</span>
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313 300 <span class="i">$Molecule</span><span class="i">-&gt;SetInputMoleculeString</span><span class="s">(</span><span class="i">$MoleculeString</span><span class="s">)</span><span class="sc">;</span>
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314 301
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315 302 <span class="k">return</span> <span class="i">$Molecule</span><span class="sc">;</span>
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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> &amp;&amp; <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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
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325 312 <span class="s">}</span>
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326 313 <span class="k">else</span> <span class="s">{</span>
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327 314 <span class="i">$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">-&gt;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">&#39;&#39;</span><span class="sc">;</span> <span class="i">$UserInitial</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span> <span class="i">$Code</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
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342 329
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343 330 <span class="i">$Code</span> = <span class="i">$Molecule</span><span class="i">-&gt;IsThreeDimensional</span><span class="s">(</span><span class="s">)</span> ? <span class="q">&#39;3D&#39;</span> <span class="co">:</span> <span class="q">&#39;2D&#39;</span><span class="sc">;</span>
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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">$Code</span><span class="s">)</span><span class="sc">;</span>
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346 333
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347 334 <span class="c"># Third line: Comments line...</span>
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348 335 <span class="k">my</span><span class="s">(</span><span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span>
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349 336 <span class="i">$Comments</span> = <span class="i">$Molecule</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;MDLComments&#39;</span><span class="s">)</span> ? <span class="i">$Molecule</span><span class="i">-&gt;GetMDLComments</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Comments&#39;</span><span class="s">)</span> ? <span class="i">$Molecule</span><span class="i">-&gt;GetComments</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="s">)</span><span class="sc">;</span>
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350 337 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdCommentsLine</span><span class="s">(</span><span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span>
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351 338
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352 339 <span class="c"># Fourth line: Counts line for V2000</span>
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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">$ChiralFlag</span><span class="s">)</span><span class="sc">;</span>
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354 341 <span class="i">$AtomCount</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetNumOfAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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355 342 <span class="i">$BondCount</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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356 343 <span class="i">$ChiralFlag</span> = <span class="n">0</span><span class="sc">;</span>
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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">$ChiralFlag</span><span class="s">)</span><span class="sc">;</span>
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358 345
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359 346 <span class="c"># Atom lines...</span>
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360 347 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomID</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">%AtomIDToNum</span><span class="s">)</span><span class="sc">;</span>
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361 348 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomAliasPropertyValue</span><span class="cm">,</span> <span class="i">@IsotopePropertyValuePairs</span><span class="cm">,</span> <span class="i">@ChargePropertyValuePairs</span><span class="cm">,</span> <span class="i">@RadicalPropertyValuePairs</span><span class="cm">,</span> <span class="i">@AtomAliasPropertyValuePairs</span><span class="s">)</span><span class="sc">;</span>
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362 349
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363 350 <span class="i">@ChargePropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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364 351 <span class="i">@IsotopePropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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365 352 <span class="i">@RadicalPropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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366 353 <span class="i">@AtomAliasPropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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367 354
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368 355 <span class="i">@Atoms</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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369 356
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370 357 <span class="i">$AtomNum</span> = <span class="n">0</span><span class="sc">;</span>
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371 358 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
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372 359 <span class="i">$AtomNum</span>++<span class="sc">;</span>
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373 360 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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374 361 <span class="i">$AtomIDToNum</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomNum</span><span class="sc">;</span>
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375 362
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376 363 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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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">-&gt;GetXYZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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378 365
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379 366 <span class="c"># Setup mass difference...</span>
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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>
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381 368 <span class="k">if</span> <span class="s">(</span><span class="i">$MassDifference</span><span class="s">)</span> <span class="s">{</span>
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382 369 <span class="c"># Hold it for M ISO property lines...</span>
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383 370 <span class="i">$IsotopePropertyValue</span> = <span class="i">_GetIsotopePropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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384 371 <span class="k">if</span> <span class="s">(</span><span class="i">$IsotopePropertyValue</span><span class="s">)</span> <span class="s">{</span>
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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>
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386 373 <span class="s">}</span>
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387 374 <span class="s">}</span>
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388 375
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389 376 <span class="c"># Setup charge...</span>
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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>
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391 378 <span class="k">if</span> <span class="s">(</span><span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span>
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392 379 <span class="c"># Hold it for M CHG property lines...</span>
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393 380 <span class="i">$ChargePropertyValue</span> = <span class="i">_GetChargePropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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394 381 <span class="k">if</span> <span class="s">(</span><span class="i">$ChargePropertyValue</span><span class="s">)</span> <span class="s">{</span>
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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>
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396 383 <span class="s">}</span>
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397 384 <span class="s">}</span>
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398 385
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399 386 <span class="c"># Hold any radical values for for M RAD property lines...</span>
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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>
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401 388 <span class="k">if</span> <span class="s">(</span><span class="i">$RadicalPropertyValue</span><span class="s">)</span> <span class="s">{</span>
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402 389 <span class="k">push</span> <span class="i">@RadicalPropertyValuePairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$RadicalPropertyValue</span><span class="s">)</span><span class="sc">;</span>
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403 390 <span class="s">}</span>
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404 391
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405 392 <span class="c"># Hold any atom alias value for A xxx property lines....</span>
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406 393 <span class="i">$AtomAliasPropertyValue</span> = <span class="i">_GetAtomAliasPropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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407 394 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomAliasPropertyValue</span><span class="s">)</span> <span class="s">{</span>
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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>
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409 396
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410 397 <span class="c"># Set AtomSymbol to carbon as atom alias would override its value during parsing...</span>
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411 398 <span class="i">$AtomSymbol</span> = <span class="q">&quot;C&quot;</span><span class="sc">;</span>
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412 399 <span class="s">}</span>
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413 400
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414 401 <span class="c"># Setup stereo parity...</span>
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415 402 <span class="i">$StereoParity</span> = <span class="i">_GetStereoParity</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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416 403
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417 404 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdAtomLine</span><span class="s">(</span><span class="i">$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>
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418 405 <span class="s">}</span>
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419 406
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420 407 <span class="c"># Bond lines...</span>
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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">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
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422 409 <span class="k">for</span> <span class="i">$FirstAtom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
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423 410 <span class="i">$FirstAtomID</span> = <span class="i">$FirstAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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424 411 <span class="i">$FirstAtomNum</span> = <span class="i">$AtomIDToNum</span>{<span class="i">$FirstAtomID</span>}<span class="sc">;</span>
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425 412
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426 413 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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427 414 <span class="i">@Bonds</span> = <span class="i">$FirstAtom</span><span class="i">-&gt;GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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428 415 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
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429 416 <span class="i">$SecondAtom</span> = <span class="i">$Bond</span><span class="i">-&gt;GetBondedAtom</span><span class="s">(</span><span class="i">$FirstAtom</span><span class="s">)</span><span class="sc">;</span>
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430 417 <span class="i">$SecondAtomID</span> = <span class="i">$SecondAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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431 418 <span class="i">$SecondAtomNum</span> = <span class="i">$AtomIDToNum</span>{<span class="i">$SecondAtomID</span>}<span class="sc">;</span>
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432 419 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomNum</span> &gt;= <span class="i">$SecondAtomNum</span><span class="s">)</span> <span class="s">{</span>
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433 420 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
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434 421 <span class="s">}</span>
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435 422 <span class="c"># Setup BondType...</span>
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436 423 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">-&gt;GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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437 424 <span class="i">$BondType</span> = <span class="i">$Bond</span><span class="i">-&gt;GetBondType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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438 425 <span class="i">$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>
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439 426
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440 427 <span class="c"># Setup BondStereo...</span>
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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>
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442 429
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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>
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444 431 <span class="s">}</span>
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445 432 <span class="s">}</span>
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446 433 <span class="c"># Property lines...</span>
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447 434 <span class="k">if</span> <span class="s">(</span><span class="i">@IsotopePropertyValuePairs</span><span class="s">)</span> <span class="s">{</span>
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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>
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449 436 <span class="s">}</span>
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450 437 <span class="k">if</span> <span class="s">(</span><span class="i">@ChargePropertyValuePairs</span><span class="s">)</span> <span class="s">{</span>
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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>
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452 439 <span class="s">}</span>
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453 440 <span class="k">if</span> <span class="s">(</span><span class="i">@RadicalPropertyValuePairs</span><span class="s">)</span> <span class="s">{</span>
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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>
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455 442 <span class="s">}</span>
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456 443 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomAliasPropertyValuePairs</span><span class="s">)</span> <span class="s">{</span>
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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>
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458 445 <span class="s">}</span>
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459 446
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460 447 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="q">&quot;M END&quot;</span><span class="sc">;</span>
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461 448
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462 449 <span class="k">return</span> <span class="k">join</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">@MoleculeLines</span><span class="sc">;</span>
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463 450 <span class="s">}</span>
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464 451
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465 452 <span class="c"># Process MassDifference value and set atom&#39;s mass number...</span>
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466 453 <span class="c">#</span>
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467 <a name="_ProcessMassDifference-"></a> 454 <span class="k">sub </span><span class="m">_ProcessMassDifference</span> <span class="s">{</span>
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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>
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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">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
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470 457
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471 458 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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472 459
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473 460 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
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474 461 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_ProcessMassDifference: Ignoring specified mass difference value, $MassDifference, in SD file: Assigned to non standard element...&quot;</span><span class="sc">;</span>
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475 462 <span class="k">return</span><span class="sc">;</span>
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476 463 <span class="s">}</span>
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477 464 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">-&gt;GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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478 465 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MassDifference</span><span class="s">)</span> <span class="s">{</span>
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479 466 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_ProcessMassDifference: Ignoring specified mass difference value, $MassDifference, in SD file: Unknown MassNumber value...&quot;</span><span class="sc">;</span>
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480 467 <span class="k">return</span><span class="sc">;</span>
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481 468 <span class="s">}</span>
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482 469 <span class="i">$NewMassNumber</span> = <span class="i">$MassNumber</span> + <span class="i">$MassDifference</span><span class="sc">;</span>
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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>
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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">-&gt;GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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485 472 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_ProcessMassDifference: Unknown mass number, $MassNumber, corresponding to specified mass difference value, $MassDifference, in SD for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. The mass number value has been assigned. Don&#39;t forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...\n&quot;</span><span class="sc">;</span>
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486 473 <span class="s">}</span>
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487 474
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488 475 <span class="c"># Use SetProperty method instead of SetMassNumber to skip explicit checks on MassNumber value...</span>
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489 476 <span class="i">$Atom</span><span class="i">-&gt;SetProperty</span><span class="s">(</span><span class="q">&#39;MassNumber&#39;</span><span class="cm">,</span> <span class="i">$NewMassNumber</span><span class="s">)</span><span class="sc">;</span>
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490 477 <span class="s">}</span>
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491 478
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492 479 <span class="c"># Get mass difference value...</span>
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493 <a name="_GetMassDifference-"></a> 480 <span class="k">sub </span><span class="m">_GetMassDifference</span> <span class="s">{</span>
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494 481 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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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>
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496 483
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497 484 <span class="i">$MassDifference</span> = <span class="n">0</span><span class="sc">;</span>
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498 485 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">-&gt;GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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499 486 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$MassNumber</span><span class="s">)</span> <span class="s">{</span>
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500 487 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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501 488 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
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502 489 <span class="i">$MostAbundantMassNumber</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
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503 490 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$MostAbundantMassNumber</span><span class="s">)</span> &amp;&amp; <span class="i">$MassNumber</span> != <span class="i">$MostAbundantMassNumber</span><span class="s">)</span> <span class="s">{</span>
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504 491 <span class="i">$MassDifference</span> = <span class="i">$MassNumber</span> - <span class="i">$MostAbundantMassNumber</span><span class="sc">;</span>
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505 492 <span class="s">}</span>
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506 493 <span class="s">}</span>
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507 494 <span class="s">}</span>
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508 495 <span class="k">return</span> <span class="i">$MassDifference</span><span class="sc">;</span>
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509 496 <span class="s">}</span>
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510 497
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511 498 <span class="c"># Process formal charge value and assign it to atom as formal charge...</span>
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512 <a name="_ProcessCharge-"></a> 499 <span class="k">sub </span><span class="m">_ProcessCharge</span> <span class="s">{</span>
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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>
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514 501 <span class="k">my</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span>
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515 502
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516 503 <span class="i">$InternalCharge</span> = <span class="i">SDFileUtil::MDLChargeToInternalCharge</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span>
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517 504 <span class="i">$Atom</span><span class="i">-&gt;SetFormalCharge</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span>
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518 505 <span class="s">}</span>
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519 506
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520 507 <span class="c"># Get MDL formal charge value ...</span>
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521 <a name="_GetCharge-"></a> 508 <span class="k">sub </span><span class="m">_GetCharge</span> <span class="s">{</span>
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522 509 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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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>
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524 511
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525 512 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span>
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526 513 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;FormalCharge&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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527 514 <span class="i">$InternalCharge</span> = <span class="i">$Atom</span><span class="i">-&gt;GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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528 515 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span> <span class="s">{</span>
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529 516 <span class="i">$Charge</span> = <span class="i">SDFileUtil::InternalChargeToMDLCharge</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span>
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530 517 <span class="s">}</span>
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531 518 <span class="s">}</span>
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532 519 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span>
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533 520 <span class="s">}</span>
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534 521
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535 522 <span class="c"># Process stereo parity value and assign it to atom as MDL property...</span>
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536 523 <span class="c">#</span>
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537 524 <span class="c"># Notes:</span>
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538 525 <span class="c"># . Mark atom as chiral center</span>
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539 526 <span class="c"># . Assign any explicit Clockwise (parity 1), CounterClockwise (parity 2) or either value (parity 3) as property of atom.</span>
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540 527 <span class="c"># . MDL values of Clockwise and CounterClockwise don&#39;t correspond to priority assigned to ligands around</span>
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541 528 <span class="c"># stereo center using CIP scheme; consequently, these values can&#39;t be used to set internal Stereochemistry for</span>
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542 529 <span class="c"># an atom.</span>
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543 530 <span class="c">#</span>
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544 <a name="_ProcessStereoParity-"></a> 531 <span class="k">sub </span><span class="m">_ProcessStereoParity</span> <span class="s">{</span>
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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>
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546 533
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547 534 <span class="i">$Atom</span><span class="i">-&gt;SetStereoCenter</span><span class="s">(</span><span class="q">&#39;1&#39;</span><span class="s">)</span><span class="sc">;</span>
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548 535 <span class="i">$Atom</span><span class="i">-&gt;SetMDLStereoParity</span><span class="s">(</span><span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span>
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549 536 <span class="s">}</span>
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550 537
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551 538 <span class="c"># Set stereo parity value to zero for now: The current release of MayaChemTools hasn&#39;t implemented</span>
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552 539 <span class="c"># functionality to determine chirality.</span>
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553 540 <span class="c">#</span>
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554 <a name="_GetStereoParity-"></a> 541 <span class="k">sub </span><span class="m">_GetStereoParity</span> <span class="s">{</span>
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555 542 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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556 543 <span class="k">my</span><span class="s">(</span><span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span>
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557 544
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558 545 <span class="i">$StereoParity</span> = <span class="n">0</span><span class="sc">;</span>
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559 546
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560 547 <span class="k">return</span> <span class="i">$StereoParity</span><span class="sc">;</span>
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561 548 <span class="s">}</span>
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diff changeset
562 549
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
563 550 <span class="c"># Process bond stereo value...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
564 <a name="_ProcessBondStereo-"></a> 551 <span class="k">sub </span><span class="m">_ProcessBondStereo</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
565 552 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
566 553 <span class="k">my</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
567 554
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
569 556 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
570 557 <span class="i">$Bond</span><span class="i">-&gt;SetBondStereochemistry</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
571 558 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
572 559 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
573 560
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
574 561 <span class="c"># Get MDLBondStereo value...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
575 <a name="_GetBondStereo-"></a> 562 <span class="k">sub </span><span class="m">_GetBondStereo</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
576 563 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
578 565
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
579 566 <span class="i">$BondStereo</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
580 567
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
581 568 <span class="i">$InternalBondStereo</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
582 569 <span class="j">BONDSTEREO:</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
583 570 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsUp</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
584 571 <span class="i">$InternalBondStereo</span> = <span class="q">&#39;Up&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
585 572 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
586 573 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
587 574 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsDown</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
588 575 <span class="i">$InternalBondStereo</span> = <span class="q">&#39;Down&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
589 576 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
590 577 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
591 578 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsUpOrDown</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
592 579 <span class="i">$InternalBondStereo</span> = <span class="q">&#39;UpOrDown&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
593 580 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
594 581 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
595 582 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsCisOrTrans</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">-&gt;IsCis</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">-&gt;IsTrans</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
596 583 <span class="i">$InternalBondStereo</span> = <span class="q">&#39;CisOrTrans&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
597 584 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
598 585 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
599 586 <span class="i">$InternalBondStereo</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
600 587 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
601 588
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
602 589 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
604 591 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
605 592
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
606 593 <span class="k">return</span> <span class="i">$BondStereo</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
607 594 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
608 595
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
609 596 <span class="c"># Zero out charge and radical values specified for atoms...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
610 <a name="_ZeroOutAtomsChargeAndRadicalValues-"></a> 597 <span class="k">sub </span><span class="m">_ZeroOutAtomsChargeAndRadicalValues</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
611 598 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
612 599 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
613 600
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
614 601 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="k">values</span> <span class="i">%</span>{<span class="i">$AtomNumToAtomMapRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
615 602 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;FormalCharge&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
616 603 <span class="i">$Atom</span><span class="i">-&gt;DeleteProperty</span><span class="s">(</span><span class="q">&#39;FormalCharge&#39;</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
617 604 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
618 605 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;SpinMultiplicity&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
619 606 <span class="i">$Atom</span><span class="i">-&gt;DeleteProperty</span><span class="s">(</span><span class="q">&#39;SpinMultiplicity&#39;</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
620 607 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
621 608 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
622 609 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
623 610
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
624 611 <span class="c"># Process charge property value pairs...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
625 <a name="_ProcessChargeProperty-"></a> 612 <span class="k">sub </span><span class="m">_ProcessChargeProperty</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
626 613 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
627 614
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
628 615 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> &amp;&amp; <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
629 616 <span class="k">return</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
630 617 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
631 618 <span class="k">my</span><span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
632 619
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
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> &lt; <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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
635 622 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$Charge</span> = <span class="i">$ValuePairsRef</span>-&gt;[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
636 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
637 624 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
638 625 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
639 626 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>-&gt;{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
640 627 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
641 628 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
642 629 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>-&gt;{<span class="i">$AtomNum</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
643 630 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;SpinMultiplicity&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
644 631 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_ProcessChargeProperty: Setting formal charge on atom number, $AtomNum, with already assigned spin multiplicity value...&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
645 632 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
646 633 <span class="i">$Atom</span><span class="i">-&gt;SetFormalCharge</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
647 634 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
648 635 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
649 636
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
650 637 <span class="c"># Get charge property value for an atom...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
651 <a name="_GetChargePropertyValue-"></a> 638 <span class="k">sub </span><span class="m">_GetChargePropertyValue</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
652 639 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
653 640 <span class="k">my</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
654 641
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
655 642 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
656 643 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;FormalCharge&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
657 644 <span class="i">$Charge</span> = <span class="i">$Atom</span><span class="i">-&gt;GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
658 645 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
659 646 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
660 647 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
661 648
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
662 649 <span class="c"># Process charge property value pairs...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
663 <a name="_ProcessRadicalProperty-"></a> 650 <span class="k">sub </span><span class="m">_ProcessRadicalProperty</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
665 652
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
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">$ValuePairsRef</span><span class="s">)</span> &amp;&amp; <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
667 654 <span class="k">return</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
668 655 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
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>
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deepakjadmin
parents:
diff changeset
670 657
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
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> &lt; <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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
673 660 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$Radical</span> = <span class="i">$ValuePairsRef</span>-&gt;[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
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parents:
diff changeset
674 661 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Radical</span><span class="s">)</span> <span class="s">{</span>
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675 662 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
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676 663 <span class="s">}</span>
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677 664 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>-&gt;{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span>
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diff changeset
678 665 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
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diff changeset
679 666 <span class="s">}</span>
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680 667 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>-&gt;{<span class="i">$AtomNum</span>}<span class="sc">;</span>
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681 668 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;FormalCharge&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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682 669 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_ProcessRadicalProperty: Setting spin multiplicity on atom number, $AtomNum, with already assigned formal charge value...&quot;</span><span class="sc">;</span>
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683 670 <span class="s">}</span>
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684 671 <span class="i">$SpinMultiplicity</span> = <span class="i">SDFileUtil::MDLRadicalToInternalSpinMultiplicity</span><span class="s">(</span><span class="i">$Radical</span><span class="s">)</span><span class="sc">;</span>
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parents:
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685 672 <span class="i">$Atom</span><span class="i">-&gt;SetSpinMultiplicity</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span>
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686 673 <span class="s">}</span>
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687 674 <span class="s">}</span>
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688 675
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689 676 <span class="c"># Get radical property value for an atom...</span>
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690 <a name="_GetRadicalPropertyValue-"></a> 677 <span class="k">sub </span><span class="m">_GetRadicalPropertyValue</span> <span class="s">{</span>
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691 678 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
diff changeset
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>
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693 680
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694 681 <span class="i">$Radical</span> = <span class="n">0</span><span class="sc">;</span>
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695 682 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;SpinMultiplicity&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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696 683 <span class="i">$SpinMultiplicity</span> = <span class="i">$Atom</span><span class="i">-&gt;GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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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>
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698 685 <span class="s">}</span>
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699 686 <span class="k">return</span> <span class="i">$Radical</span><span class="sc">;</span>
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700 687 <span class="s">}</span>
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701 688
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702 689 <span class="c"># Process isotope property value pairs...</span>
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703 <a name="_ProcessIsotopeProperty-"></a> 690 <span class="k">sub </span><span class="m">_ProcessIsotopeProperty</span> <span class="s">{</span>
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704 691 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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705 692
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706 693 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> &amp;&amp; <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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707 694 <span class="k">return</span><span class="sc">;</span>
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diff changeset
708 695 <span class="s">}</span>
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709 696 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
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710 697
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711 698 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span>
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712 699 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> &lt; <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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713 700 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$MassNumber</span> = <span class="i">$ValuePairsRef</span>-&gt;[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
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714 701 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MassNumber</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
715 702 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
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diff changeset
716 703 <span class="s">}</span>
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717 704 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>-&gt;{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
718 705 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
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diff changeset
719 706 <span class="s">}</span>
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diff changeset
720 707 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>-&gt;{<span class="i">$AtomNum</span>}<span class="sc">;</span>
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721 708 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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722 709
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723 710 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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724 711 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
725 712 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_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, $AtomSymbol. The mass number value has been assigned. Don&#39;t forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...\n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
726 713 <span class="s">}</span>
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diff changeset
727 714
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diff changeset
728 715 <span class="c"># Use SetProperty method instead of SetMassNumber to skip explicit checks on MassNumber value...</span>
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diff changeset
729 716 <span class="i">$Atom</span><span class="i">-&gt;SetProperty</span><span class="s">(</span><span class="q">&#39;MassNumber&#39;</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
730 717 <span class="s">}</span>
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diff changeset
731 718 <span class="s">}</span>
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diff changeset
732 719
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diff changeset
733 720 <span class="c"># Get isotope property value for an atom...</span>
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diff changeset
734 <a name="_GetIsotopePropertyValue-"></a> 721 <span class="k">sub </span><span class="m">_GetIsotopePropertyValue</span> <span class="s">{</span>
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diff changeset
735 722 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
736 723 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
737 724
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738 725 <span class="i">$MassNumber</span> = <span class="n">0</span><span class="sc">;</span>
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739 726 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;MassNumber&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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740 727 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">-&gt;GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
741 728 <span class="s">}</span>
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diff changeset
742 729 <span class="k">return</span> <span class="i">$MassNumber</span><span class="sc">;</span>
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diff changeset
743 730 <span class="s">}</span>
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diff changeset
744 731
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diff changeset
745 732 <span class="c"># Process atom alias property value pairs...</span>
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diff changeset
746 <a name="_ProcessAtomAliasProperty-"></a> 733 <span class="k">sub </span><span class="m">_ProcessAtomAliasProperty</span> <span class="s">{</span>
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diff changeset
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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diff changeset
748 735
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diff changeset
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">$ValuePairsRef</span><span class="s">)</span> &amp;&amp; <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
750 737 <span class="k">return</span><span class="sc">;</span>
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diff changeset
751 738 <span class="s">}</span>
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diff changeset
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">$Atom</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
753 740
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diff changeset
754 741 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span>
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diff changeset
755 742 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> &lt; <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
756 743 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$AtomAlias</span> = <span class="i">$ValuePairsRef</span>-&gt;[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
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diff changeset
757 744 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomNum</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
758 745 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
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diff changeset
759 746 <span class="s">}</span>
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diff changeset
760 747 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>-&gt;{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span>
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diff changeset
761 748 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
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diff changeset
762 749 <span class="s">}</span>
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diff changeset
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>
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diff changeset
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>
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diff changeset
765 752 <span class="i">carp</span><span class="s">(</span><span class="q">&quot;Warning: ${ClassName}-&gt;_ProcessAtomAliasProperty: Ignoring atom alias property line: No Atom alias value specified...&quot;</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
766 753 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span>
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diff changeset
767 754 <span class="s">}</span>
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diff changeset
768 755
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diff changeset
769 756 <span class="c"># Set atom symbol to atom alias which sets atomic number automatically...</span>
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diff changeset
770 757 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>-&gt;{<span class="i">$AtomNum</span>}<span class="sc">;</span>
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diff changeset
771 758 <span class="i">$Atom</span><span class="i">-&gt;SetAtomSymbol</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
772 759
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diff changeset
773 760 <span class="i">$Atom</span><span class="i">-&gt;SetProperty</span><span class="s">(</span><span class="q">&#39;AtomAlias&#39;</span><span class="cm">,</span> <span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
774 761 <span class="s">}</span>
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775 762 <span class="s">}</span>
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776 763
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diff changeset
777 764 <span class="c"># Get atom alias property value for an atom...</span>
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diff changeset
778 <a name="_GetAtomAliasPropertyValue-"></a> 765 <span class="k">sub </span><span class="m">_GetAtomAliasPropertyValue</span> <span class="s">{</span>
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diff changeset
779 766 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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780 767 <span class="k">my</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
781 768
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diff changeset
782 769 <span class="i">$AtomAlias</span> = <span class="k">undef</span><span class="sc">;</span>
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diff changeset
783 770 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;AtomAlias&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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784 771 <span class="i">$AtomAlias</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomAlias</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
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785 772 <span class="s">}</span>
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parents:
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786 773 <span class="k">return</span> <span class="i">$AtomAlias</span><span class="sc">;</span>
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parents:
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787 774 <span class="s">}</span>
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788 775
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789 776 <span class="c"># Is it a MDLMolFileIO object?</span>
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790 <a name="_IsMDLMolFileIO-"></a> 777 <span class="k">sub </span><span class="m">_IsMDLMolFileIO</span> <span class="s">{</span>
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parents:
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791 778 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
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792 779
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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">$Object</span><span class="s">)</span> &amp;&amp; <span class="i">$Object</span><span class="i">-&gt;isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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parents:
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794 781 <span class="s">}</span>
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795 782
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796 783
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797 <a name="EOF-"></a></pre>
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798 <p>&nbsp;</p>
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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>