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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/MDLMolFileIO.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,804 @@ +<html> +<head> +<title>MayaChemTools:Code:FileIO::MDLMolFileIO.pm</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> +<a name="package-FileIO::MDLMolFileIO-"></a> 1 <span class="k">package </span><span class="i">FileIO::MDLMolFileIO</span><span class="sc">;</span> + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: MDLMolFileIO.pm,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:48:43 $</span> + 5 <span class="c"># $Revision: 1.32 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">SDFileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">FileIO::FileIO</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> + 38 + 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> + 40 + 41 <span class="i">@ISA</span> = <span class="q">qw(FileIO::FileIO Exporter)</span><span class="sc">;</span> + 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> + 43 <span class="i">@EXPORT_OK</span> = <span class="q">qw(IsMDLMolFile)</span><span class="sc">;</span> + 44 + 45 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> + 46 + 47 <span class="c"># Setup class variables...</span> + 48 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> + 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 50 + 51 <span class="c"># Class constructor...</span> +<a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> + 53 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 54 + 55 <span class="c"># Initialize object...</span> + 56 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 57 <span class="k">bless</span> <span class="i">$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> + 58 <span class="i">$This</span><span class="i">->_InitializeMDLMolFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 59 + 60 <span class="i">$This</span><span class="i">->_InitializeMDLMolFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> + 61 + 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 63 <span class="s">}</span> + 64 + 65 <span class="c"># Initialize any local object data...</span> + 66 <span class="c">#</span> +<a name="_InitializeMDLMolFileIO-"></a> 67 <span class="k">sub </span><span class="m">_InitializeMDLMolFileIO</span> <span class="s">{</span> + 68 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 69 + 70 <span class="c"># Nothing to do: Base class FileIO handles default class variables...</span> + 71 + 72 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 73 <span class="s">}</span> + 74 + 75 <span class="c"># Initialize class ...</span> +<a name="_InitializeClass-"></a> 76 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> + 77 <span class="c">#Class name...</span> + 78 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> + 79 + 80 <span class="s">}</span> + 81 + 82 <span class="c"># Initialize object values...</span> +<a name="_InitializeMDLMolFileIOProperties-"></a> 83 <span class="k">sub </span><span class="m">_InitializeMDLMolFileIOProperties</span> <span class="s">{</span> + 84 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 85 + 86 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> + 87 <span class="c"># are implemented on-demand using ObjectProperty class.</span> + 88 + 89 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 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> + 91 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> + 92 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 93 <span class="s">}</span> + 94 + 95 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="s">)</span> <span class="s">{</span> + 96 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying file name..."</span><span class="sc">;</span> + 97 <span class="s">}</span> + 98 + 99 <span class="c"># Make sure it's a MDLMol file...</span> + 100 <span class="i">$Name</span> = <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="sc">;</span> + 101 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsMDLMolFile</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 102 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $Name, doesn't appear to be MDLMol format..."</span><span class="sc">;</span> + 103 <span class="s">}</span> + 104 + 105 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 106 <span class="s">}</span> + 107 + 108 <span class="c"># Is it a MDLMol file?</span> +<a name="IsMDLMolFile-"></a> 109 <span class="k">sub </span><span class="m">IsMDLMolFile ($;$)</span> <span class="s">{</span> + 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> + 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">$Status</span><span class="s">)</span><span class="sc">;</span> + 112 + 113 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMDLMolFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 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> + 115 <span class="s">}</span> + 116 <span class="k">else</span> <span class="s">{</span> + 117 <span class="i">$FileName</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> + 118 <span class="s">}</span> + 119 + 120 <span class="c"># Check file extension...</span> + 121 <span class="i">$Status</span> = <span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"mol"</span><span class="s">)</span><span class="sc">;</span> + 122 + 123 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> + 124 <span class="s">}</span> + 125 + 126 <span class="c"># Read molecule from file and return molecule object...</span> +<a name="ReadMolecule-"></a> 127 <span class="k">sub </span><span class="m">ReadMolecule</span> <span class="s">{</span> + 128 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 129 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> + 130 + 131 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 132 <span class="k">return</span> <span class="i">$This</span><span class="i">->ParseMoleculeString</span><span class="s">(</span><span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> + 133 <span class="s">}</span> + 134 + 135 <span class="c"># Write compound data using Molecule object...</span> +<a name="WriteMolecule-"></a> 136 <span class="k">sub </span><span class="m">WriteMolecule</span> <span class="s">{</span> + 137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 138 + 139 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> && <span class="i">$Molecule</span><span class="i">->IsMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 140 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->WriteMolecule: No data written: Molecule object is not specified..."</span><span class="sc">;</span> + 141 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 142 <span class="s">}</span> + 143 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> + 144 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 145 + 146 <span class="k">print</span> <span class="i">$FileHandle</span> <span class="i">$This</span><span class="i">->GenerateMoleculeString</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> . <span class="q">"\n"</span><span class="sc">;</span> + 147 + 148 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 149 <span class="s">}</span> + 150 + 151 <span class="c"># Retrieve molecule string...</span> +<a name="ReadMoleculeString-"></a> 152 <span class="k">sub </span><span class="m">ReadMoleculeString</span> <span class="s">{</span> + 153 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 154 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> + 155 + 156 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 157 <span class="k">return</span> <span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> + 158 <span class="s">}</span> + 159 + 160 <span class="c"># Parse molecule string and return molecule object. ParseMoleculeString supports two invocation methods: class</span> + 161 <span class="c"># method or a package function.</span> + 162 <span class="c">#</span> +<a name="ParseMoleculeString-"></a> 163 <span class="k">sub </span><span class="m">ParseMoleculeString</span> <span class="s">{</span> + 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> + 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> + 166 + 167 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMDLMolFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 168 <span class="s">(</span><span class="i">$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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> + 169 <span class="s">}</span> + 170 <span class="k">else</span> <span class="s">{</span> + 171 <span class="i">$MoleculeString</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> + 172 <span class="i">$This</span> = <span class="k">undef</span><span class="sc">;</span> + 173 <span class="s">}</span> + 174 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MoleculeString</span><span class="s">)</span> <span class="s">{</span> + 175 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 176 <span class="s">}</span> + 177 <span class="k">my</span><span class="s">(</span><span class="i">$LineIndex</span><span class="cm">,</span> <span class="i">@MoleculeLines</span><span class="s">)</span><span class="sc">;</span> + 178 <span class="i">@MoleculeLines</span> = <span class="k">split</span> <span class="q">/\n/</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="sc">;</span> + 179 + 180 <span class="c"># Create molecule object and set molecule level native and MDL properties...</span> + 181 <span class="c">#</span> + 182 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> + 183 <span class="i">$Molecule</span> = <span class="i">new</span> <span class="i">Molecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 184 + 185 <span class="c"># Set valence model for calculating implicit hydrogens...</span> + 186 <span class="i">$Molecule</span><span class="i">->SetValenceModel</span><span class="s">(</span><span class="q">'MDLValenceModel'</span><span class="s">)</span><span class="sc">;</span> + 187 + 188 <span class="c"># Process headers data...</span> + 189 <span class="i">$LineIndex</span> = <span class="n">0</span><span class="sc">;</span> + 190 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 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> + 192 <span class="i">$Molecule</span><span class="i">->SetName</span><span class="s">(</span><span class="i">$MoleculeName</span><span class="s">)</span><span class="sc">;</span> + 193 + 194 <span class="i">$LineIndex</span>++<span class="sc">;</span> + 195 <span class="k">my</span><span class="s">(</span><span class="i">$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">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span> + 196 <span class="i">$Molecule</span><span class="i">->SetProperties</span><span class="s">(</span><span class="q">'MDLUserInitial'</span> <span class="cm">=></span> <span class="i">$UserInitial</span><span class="cm">,</span> <span class="q">'MDLProgramName'</span> <span class="cm">=></span> <span class="i">$ProgramName</span><span class="cm">,</span> <span class="q">'MDLDate'</span> <span class="cm">=></span> <span class="i">$Date</span><span class="cm">,</span> <span class="q">'MDLCode'</span> <span class="cm">=></span> <span class="i">$Code</span><span class="cm">,</span> <span class="q">'MDLScalingFactor1'</span> <span class="cm">=></span> <span class="i">$ScalingFactor1</span><span class="cm">,</span> <span class="q">'MDLScalingFactor2'</span> <span class="cm">=></span> <span class="i">$ScalingFactor2</span><span class="cm">,</span> <span class="q">'MDLEnergy'</span> <span class="cm">=></span> <span class="i">$Energy</span><span class="cm">,</span> <span class="q">'MDLRegistryNum'</span> <span class="cm">=></span> <span class="i">$RegistryNum</span><span class="s">)</span><span class="sc">;</span> + 197 + 198 <span class="i">$LineIndex</span>++<span class="sc">;</span> + 199 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 200 <span class="i">$Molecule</span><span class="i">->SetProperties</span><span class="s">(</span><span class="q">'MDLComments'</span> <span class="cm">=></span> <span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span> + 201 + 202 <span class="i">$LineIndex</span>++<span class="sc">;</span> + 203 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 204 + 205 <span class="i">$Molecule</span><span class="i">->SetProperties</span><span class="s">(</span><span class="q">'MDLChiralFlag'</span> <span class="cm">=></span> <span class="i">$ChiralFlag</span><span class="cm">,</span> <span class="q">'MDLPropertyCount'</span> <span class="cm">=></span> <span class="i">$PropertyCount</span><span class="cm">,</span> <span class="q">'MDLVersion'</span> <span class="cm">=></span> <span class="i">$Version</span><span class="s">)</span><span class="sc">;</span> + 206 + 207 <span class="c"># Process atom data...</span> + 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">$Atom</span><span class="cm">,</span> <span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> + 209 + 210 <span class="i">$AtomNum</span> = <span class="n">0</span><span class="sc">;</span> + 211 <span class="i">%AtomNumToAtomMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 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> + 213 + 214 <span class="k">for</span> <span class="s">(</span><span class="i">$LineIndex</span> = <span class="i">$FirstAtomLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span> <= <span class="i">$LastAtomLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span>++<span class="s">)</span> <span class="s">{</span> + 215 <span class="i">$AtomNum</span>++<span class="sc">;</span> + 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">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span> + 217 + 218 <span class="i">$Atom</span> = <span class="i">new</span> <span class="i">Atom</span><span class="s">(</span><span class="q">'AtomSymbol'</span> <span class="cm">=></span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="q">'XYZ'</span> <span class="cm">=></span> <span class="s">[</span><span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> + 219 + 220 <span class="k">if</span> <span class="s">(</span><span class="i">$MassDifference</span> && <span class="i">$MassDifference</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> + 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> + 222 <span class="s">}</span> + 223 <span class="k">if</span> <span class="s">(</span><span class="i">$Charge</span> && <span class="i">$Charge</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> + 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> + 225 <span class="s">}</span> + 226 <span class="k">if</span> <span class="s">(</span><span class="i">$StereoParity</span> && <span class="i">$StereoParity</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> + 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> + 228 <span class="s">}</span> + 229 + 230 <span class="i">$AtomNumToAtomMap</span>{<span class="i">$AtomNum</span>} = <span class="i">$Atom</span><span class="sc">;</span> + 231 <span class="i">$Molecule</span><span class="i">->AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> + 232 <span class="s">}</span> + 233 + 234 <span class="c"># Process bond data...</span> + 235 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 236 + 237 <span class="i">$FirstBondLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span><span class="sc">;</span> + 238 <span class="i">$LastBondLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span> + <span class="i">$BondCount</span> - <span class="n">1</span><span class="sc">;</span> + 239 + 240 <span class="k">for</span> <span class="s">(</span><span class="i">$LineIndex</span> = <span class="i">$FirstBondLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span> <= <span class="i">$LastBondLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span>++<span class="s">)</span> <span class="s">{</span> + 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> + 242 + 243 <span class="i">$Atom1</span> = <span class="i">$AtomNumToAtomMap</span>{<span class="i">$FirstAtomNum</span>}<span class="sc">;</span> + 244 <span class="i">$Atom2</span> = <span class="i">$AtomNumToAtomMap</span>{<span class="i">$SecondAtomNum</span>}<span class="sc">;</span> + 245 + 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">$BondType</span><span class="s">)</span><span class="sc">;</span> + 247 <span class="i">$Bond</span> = <span class="i">new</span> <span class="i">Bond</span><span class="s">(</span><span class="q">'Atoms'</span> <span class="cm">=></span> <span class="s">[</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">]</span><span class="cm">,</span> <span class="q">'BondOrder'</span> <span class="cm">=></span> <span class="i">$InternalBondOrder</span><span class="s">)</span><span class="sc">;</span> + 248 <span class="i">$Bond</span><span class="i">->SetBondType</span><span class="s">(</span><span class="i">$InternalBondType</span><span class="s">)</span><span class="sc">;</span> + 249 + 250 <span class="k">if</span> <span class="s">(</span><span class="i">$BondStereo</span> && <span class="i">$BondStereo</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> + 251 <span class="i">_ProcessBondStereo</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span><span class="sc">;</span> + 252 <span class="s">}</span> + 253 + 254 <span class="i">$Molecule</span><span class="i">->AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> + 255 <span class="s">}</span> + 256 + 257 <span class="c"># Process available property block lines starting with A aaa, M CHG, M ISO and M RAD. All other property blocks</span> + 258 <span class="c"># lines are for query or specific display purposes and are ignored for now.</span> + 259 <span class="c">#</span> + 260 <span class="c">#</span> + 261 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 262 + 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> + 264 <span class="i">$PropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span> + 265 <span class="i">$FirstChargeOrRadicalLine</span> = <span class="n">1</span><span class="sc">;</span> + 266 + 267 <span class="j">PROPERTYLINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$PropertyLine</span> !~ <span class="q">/^M END/i</span> <span class="s">)</span> <span class="s">{</span> + 268 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span> + 269 <span class="k">last</span> <span class="j">PROPERTYLINE</span><span class="sc">;</span> + 270 <span class="s">}</span> + 271 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^(M CHG|M RAD)/i</span><span class="s">)</span> <span class="s">{</span> + 272 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstChargeOrRadicalLine</span><span class="s">)</span> <span class="s">{</span> + 273 <span class="i">$FirstChargeOrRadicalLine</span> = <span class="n">0</span><span class="sc">;</span> + 274 <span class="i">_ZeroOutAtomsChargeAndRadicalValues</span><span class="s">(</span>\<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> + 275 <span class="s">}</span> + 276 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M CHG/i</span><span class="s">)</span> <span class="s">{</span> + 277 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdChargePropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span> + 278 <span class="i">_ProcessChargeProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> + 279 <span class="s">}</span> + 280 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M RAD/i</span><span class="s">)</span> <span class="s">{</span> + 281 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdRadicalPropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span> + 282 <span class="i">_ProcessRadicalProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> + 283 <span class="s">}</span> + 284 <span class="s">}</span> + 285 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M ISO/i</span><span class="s">)</span> <span class="s">{</span> + 286 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdIsotopePropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span> + 287 <span class="i">_ProcessIsotopeProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> + 288 <span class="s">}</span> + 289 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^A /i</span><span class="s">)</span> <span class="s">{</span> + 290 <span class="k">my</span><span class="s">(</span><span class="i">$NextPropertyLine</span><span class="s">)</span><span class="sc">;</span> + 291 <span class="i">$PropertyLineIndex</span>++<span class="sc">;</span> + 292 <span class="i">$NextPropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span> + 293 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdAtomAliasPropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="cm">,</span> <span class="i">$NextPropertyLine</span><span class="s">)</span><span class="sc">;</span> + 294 <span class="i">_ProcessAtomAliasProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> + 295 <span class="s">}</span> + 296 <span class="i">$PropertyLineIndex</span>++<span class="sc">;</span> + 297 <span class="i">$PropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span> + 298 <span class="s">}</span> + 299 <span class="c"># Store input molecule string as generic property of molecule...</span> + 300 <span class="i">$Molecule</span><span class="i">->SetInputMoleculeString</span><span class="s">(</span><span class="i">$MoleculeString</span><span class="s">)</span><span class="sc">;</span> + 301 + 302 <span class="k">return</span> <span class="i">$Molecule</span><span class="sc">;</span> + 303 <span class="s">}</span> + 304 + 305 <span class="c"># Generate molecule string using molecule object...</span> +<a name="GenerateMoleculeString-"></a> 306 <span class="k">sub </span><span class="m">GenerateMoleculeString</span> <span class="s">{</span> + 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> + 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> + 309 + 310 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMDLMolFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 311 <span class="s">(</span><span class="i">$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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> + 312 <span class="s">}</span> + 313 <span class="k">else</span> <span class="s">{</span> + 314 <span class="i">$Molecule</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> + 315 <span class="i">$This</span> = <span class="k">undef</span><span class="sc">;</span> + 316 <span class="s">}</span> + 317 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 318 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 319 <span class="s">}</span> + 320 <span class="k">my</span><span class="s">(</span><span class="i">@MoleculeLines</span><span class="s">)</span><span class="sc">;</span> + 321 <span class="i">@MoleculeLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 322 + 323 <span class="c"># First line: Molname line...</span> + 324 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdMolNameLine</span><span class="s">(</span><span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> + 325 + 326 <span class="c"># Second line: Misc info...</span> + 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">$Code</span><span class="s">)</span><span class="sc">;</span> + 328 <span class="i">$ProgramName</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$UserInitial</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$Code</span> = <span class="q">''</span><span class="sc">;</span> + 329 + 330 <span class="i">$Code</span> = <span class="i">$Molecule</span><span class="i">->IsThreeDimensional</span><span class="s">(</span><span class="s">)</span> ? <span class="q">'3D'</span> <span class="co">:</span> <span class="q">'2D'</span><span class="sc">;</span> + 331 + 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">$Code</span><span class="s">)</span><span class="sc">;</span> + 333 + 334 <span class="c"># Third line: Comments line...</span> + 335 <span class="k">my</span><span class="s">(</span><span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span> + 336 <span class="i">$Comments</span> = <span class="i">$Molecule</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MDLComments'</span><span class="s">)</span> ? <span class="i">$Molecule</span><span class="i">->GetMDLComments</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Comments'</span><span class="s">)</span> ? <span class="i">$Molecule</span><span class="i">->GetComments</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span> + 337 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdCommentsLine</span><span class="s">(</span><span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span> + 338 + 339 <span class="c"># Fourth line: Counts line for V2000</span> + 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">$ChiralFlag</span><span class="s">)</span><span class="sc">;</span> + 341 <span class="i">$AtomCount</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 342 <span class="i">$BondCount</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 343 <span class="i">$ChiralFlag</span> = <span class="n">0</span><span class="sc">;</span> + 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">$ChiralFlag</span><span class="s">)</span><span class="sc">;</span> + 345 + 346 <span class="c"># Atom lines...</span> + 347 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomID</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">%AtomIDToNum</span><span class="s">)</span><span class="sc">;</span> + 348 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomAliasPropertyValue</span><span class="cm">,</span> <span class="i">@IsotopePropertyValuePairs</span><span class="cm">,</span> <span class="i">@ChargePropertyValuePairs</span><span class="cm">,</span> <span class="i">@RadicalPropertyValuePairs</span><span class="cm">,</span> <span class="i">@AtomAliasPropertyValuePairs</span><span class="s">)</span><span class="sc">;</span> + 349 + 350 <span class="i">@ChargePropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 351 <span class="i">@IsotopePropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 352 <span class="i">@RadicalPropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 353 <span class="i">@AtomAliasPropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 354 + 355 <span class="i">@Atoms</span> = <span class="i">$Molecule</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 356 + 357 <span class="i">$AtomNum</span> = <span class="n">0</span><span class="sc">;</span> + 358 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> + 359 <span class="i">$AtomNum</span>++<span class="sc">;</span> + 360 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 361 <span class="i">$AtomIDToNum</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomNum</span><span class="sc">;</span> + 362 + 363 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 364 <span class="s">(</span><span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="s">)</span> = <span class="i">$Atom</span><span class="i">->GetXYZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 365 + 366 <span class="c"># Setup mass difference...</span> + 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> + 368 <span class="k">if</span> <span class="s">(</span><span class="i">$MassDifference</span><span class="s">)</span> <span class="s">{</span> + 369 <span class="c"># Hold it for M ISO property lines...</span> + 370 <span class="i">$IsotopePropertyValue</span> = <span class="i">_GetIsotopePropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> + 371 <span class="k">if</span> <span class="s">(</span><span class="i">$IsotopePropertyValue</span><span class="s">)</span> <span class="s">{</span> + 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> + 373 <span class="s">}</span> + 374 <span class="s">}</span> + 375 + 376 <span class="c"># Setup charge...</span> + 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> + 378 <span class="k">if</span> <span class="s">(</span><span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span> + 379 <span class="c"># Hold it for M CHG property lines...</span> + 380 <span class="i">$ChargePropertyValue</span> = <span class="i">_GetChargePropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> + 381 <span class="k">if</span> <span class="s">(</span><span class="i">$ChargePropertyValue</span><span class="s">)</span> <span class="s">{</span> + 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> + 383 <span class="s">}</span> + 384 <span class="s">}</span> + 385 + 386 <span class="c"># Hold any radical values for for M RAD property lines...</span> + 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> + 388 <span class="k">if</span> <span class="s">(</span><span class="i">$RadicalPropertyValue</span><span class="s">)</span> <span class="s">{</span> + 389 <span class="k">push</span> <span class="i">@RadicalPropertyValuePairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$RadicalPropertyValue</span><span class="s">)</span><span class="sc">;</span> + 390 <span class="s">}</span> + 391 + 392 <span class="c"># Hold any atom alias value for A xxx property lines....</span> + 393 <span class="i">$AtomAliasPropertyValue</span> = <span class="i">_GetAtomAliasPropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> + 394 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomAliasPropertyValue</span><span class="s">)</span> <span class="s">{</span> + 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> + 396 + 397 <span class="c"># Set AtomSymbol to carbon as atom alias would override its value during parsing...</span> + 398 <span class="i">$AtomSymbol</span> = <span class="q">"C"</span><span class="sc">;</span> + 399 <span class="s">}</span> + 400 + 401 <span class="c"># Setup stereo parity...</span> + 402 <span class="i">$StereoParity</span> = <span class="i">_GetStereoParity</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> + 403 + 404 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdAtomLine</span><span class="s">(</span><span class="i">$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> + 405 <span class="s">}</span> + 406 + 407 <span class="c"># Bond lines...</span> + 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">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> + 409 <span class="k">for</span> <span class="i">$FirstAtom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> + 410 <span class="i">$FirstAtomID</span> = <span class="i">$FirstAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 411 <span class="i">$FirstAtomNum</span> = <span class="i">$AtomIDToNum</span>{<span class="i">$FirstAtomID</span>}<span class="sc">;</span> + 412 + 413 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 414 <span class="i">@Bonds</span> = <span class="i">$FirstAtom</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 415 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> + 416 <span class="i">$SecondAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$FirstAtom</span><span class="s">)</span><span class="sc">;</span> + 417 <span class="i">$SecondAtomID</span> = <span class="i">$SecondAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 418 <span class="i">$SecondAtomNum</span> = <span class="i">$AtomIDToNum</span>{<span class="i">$SecondAtomID</span>}<span class="sc">;</span> + 419 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomNum</span> >= <span class="i">$SecondAtomNum</span><span class="s">)</span> <span class="s">{</span> + 420 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> + 421 <span class="s">}</span> + 422 <span class="c"># Setup BondType...</span> + 423 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 424 <span class="i">$BondType</span> = <span class="i">$Bond</span><span class="i">->GetBondType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 425 <span class="i">$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> + 426 + 427 <span class="c"># Setup BondStereo...</span> + 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> + 429 + 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> + 431 <span class="s">}</span> + 432 <span class="s">}</span> + 433 <span class="c"># Property lines...</span> + 434 <span class="k">if</span> <span class="s">(</span><span class="i">@IsotopePropertyValuePairs</span><span class="s">)</span> <span class="s">{</span> + 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> + 436 <span class="s">}</span> + 437 <span class="k">if</span> <span class="s">(</span><span class="i">@ChargePropertyValuePairs</span><span class="s">)</span> <span class="s">{</span> + 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> + 439 <span class="s">}</span> + 440 <span class="k">if</span> <span class="s">(</span><span class="i">@RadicalPropertyValuePairs</span><span class="s">)</span> <span class="s">{</span> + 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> + 442 <span class="s">}</span> + 443 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomAliasPropertyValuePairs</span><span class="s">)</span> <span class="s">{</span> + 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> + 445 <span class="s">}</span> + 446 + 447 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="q">"M END"</span><span class="sc">;</span> + 448 + 449 <span class="k">return</span> <span class="k">join</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">@MoleculeLines</span><span class="sc">;</span> + 450 <span class="s">}</span> + 451 + 452 <span class="c"># Process MassDifference value and set atom's mass number...</span> + 453 <span class="c">#</span> +<a name="_ProcessMassDifference-"></a> 454 <span class="k">sub </span><span class="m">_ProcessMassDifference</span> <span class="s">{</span> + 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> + 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">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> + 457 + 458 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 459 + 460 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> + 461 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessMassDifference: Ignoring specified mass difference value, $MassDifference, in SD file: Assigned to non standard element..."</span><span class="sc">;</span> + 462 <span class="k">return</span><span class="sc">;</span> + 463 <span class="s">}</span> + 464 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 465 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MassDifference</span><span class="s">)</span> <span class="s">{</span> + 466 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessMassDifference: Ignoring specified mass difference value, $MassDifference, in SD file: Unknown MassNumber value..."</span><span class="sc">;</span> + 467 <span class="k">return</span><span class="sc">;</span> + 468 <span class="s">}</span> + 469 <span class="i">$NewMassNumber</span> = <span class="i">$MassNumber</span> + <span class="i">$MassDifference</span><span class="sc">;</span> + 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> + 471 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 472 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessMassDifference: Unknown mass number, $MassNumber, corresponding to specified mass difference value, $MassDifference, in SD for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. The mass number value has been assigned. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...\n"</span><span class="sc">;</span> + 473 <span class="s">}</span> + 474 + 475 <span class="c"># Use SetProperty method instead of SetMassNumber to skip explicit checks on MassNumber value...</span> + 476 <span class="i">$Atom</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="cm">,</span> <span class="i">$NewMassNumber</span><span class="s">)</span><span class="sc">;</span> + 477 <span class="s">}</span> + 478 + 479 <span class="c"># Get mass difference value...</span> +<a name="_GetMassDifference-"></a> 480 <span class="k">sub </span><span class="m">_GetMassDifference</span> <span class="s">{</span> + 481 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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> + 483 + 484 <span class="i">$MassDifference</span> = <span class="n">0</span><span class="sc">;</span> + 485 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 486 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$MassNumber</span><span class="s">)</span> <span class="s">{</span> + 487 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 488 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> + 489 <span class="i">$MostAbundantMassNumber</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> + 490 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$MostAbundantMassNumber</span><span class="s">)</span> && <span class="i">$MassNumber</span> != <span class="i">$MostAbundantMassNumber</span><span class="s">)</span> <span class="s">{</span> + 491 <span class="i">$MassDifference</span> = <span class="i">$MassNumber</span> - <span class="i">$MostAbundantMassNumber</span><span class="sc">;</span> + 492 <span class="s">}</span> + 493 <span class="s">}</span> + 494 <span class="s">}</span> + 495 <span class="k">return</span> <span class="i">$MassDifference</span><span class="sc">;</span> + 496 <span class="s">}</span> + 497 + 498 <span class="c"># Process formal charge value and assign it to atom as formal charge...</span> +<a name="_ProcessCharge-"></a> 499 <span class="k">sub </span><span class="m">_ProcessCharge</span> <span class="s">{</span> + 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> + 501 <span class="k">my</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span> + 502 + 503 <span class="i">$InternalCharge</span> = <span class="i">SDFileUtil::MDLChargeToInternalCharge</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span> + 504 <span class="i">$Atom</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span> + 505 <span class="s">}</span> + 506 + 507 <span class="c"># Get MDL formal charge value ...</span> +<a name="_GetCharge-"></a> 508 <span class="k">sub </span><span class="m">_GetCharge</span> <span class="s">{</span> + 509 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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> + 511 + 512 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span> + 513 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 514 <span class="i">$InternalCharge</span> = <span class="i">$Atom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 515 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span> <span class="s">{</span> + 516 <span class="i">$Charge</span> = <span class="i">SDFileUtil::InternalChargeToMDLCharge</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span> + 517 <span class="s">}</span> + 518 <span class="s">}</span> + 519 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span> + 520 <span class="s">}</span> + 521 + 522 <span class="c"># Process stereo parity value and assign it to atom as MDL property...</span> + 523 <span class="c">#</span> + 524 <span class="c"># Notes:</span> + 525 <span class="c"># . Mark atom as chiral center</span> + 526 <span class="c"># . Assign any explicit Clockwise (parity 1), CounterClockwise (parity 2) or either value (parity 3) as property of atom.</span> + 527 <span class="c"># . MDL values of Clockwise and CounterClockwise don't correspond to priority assigned to ligands around</span> + 528 <span class="c"># stereo center using CIP scheme; consequently, these values can't be used to set internal Stereochemistry for</span> + 529 <span class="c"># an atom.</span> + 530 <span class="c">#</span> +<a name="_ProcessStereoParity-"></a> 531 <span class="k">sub </span><span class="m">_ProcessStereoParity</span> <span class="s">{</span> + 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> + 533 + 534 <span class="i">$Atom</span><span class="i">->SetStereoCenter</span><span class="s">(</span><span class="q">'1'</span><span class="s">)</span><span class="sc">;</span> + 535 <span class="i">$Atom</span><span class="i">->SetMDLStereoParity</span><span class="s">(</span><span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span> + 536 <span class="s">}</span> + 537 + 538 <span class="c"># Set stereo parity value to zero for now: The current release of MayaChemTools hasn't implemented</span> + 539 <span class="c"># functionality to determine chirality.</span> + 540 <span class="c">#</span> +<a name="_GetStereoParity-"></a> 541 <span class="k">sub </span><span class="m">_GetStereoParity</span> <span class="s">{</span> + 542 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 543 <span class="k">my</span><span class="s">(</span><span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span> + 544 + 545 <span class="i">$StereoParity</span> = <span class="n">0</span><span class="sc">;</span> + 546 + 547 <span class="k">return</span> <span class="i">$StereoParity</span><span class="sc">;</span> + 548 <span class="s">}</span> + 549 + 550 <span class="c"># Process bond stereo value...</span> +<a name="_ProcessBondStereo-"></a> 551 <span class="k">sub </span><span class="m">_ProcessBondStereo</span> <span class="s">{</span> + 552 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 553 <span class="k">my</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span><span class="sc">;</span> + 554 + 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> + 556 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span> <span class="s">{</span> + 557 <span class="i">$Bond</span><span class="i">->SetBondStereochemistry</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span><span class="sc">;</span> + 558 <span class="s">}</span> + 559 <span class="s">}</span> + 560 + 561 <span class="c"># Get MDLBondStereo value...</span> +<a name="_GetBondStereo-"></a> 562 <span class="k">sub </span><span class="m">_GetBondStereo</span> <span class="s">{</span> + 563 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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> + 565 + 566 <span class="i">$BondStereo</span> = <span class="n">0</span><span class="sc">;</span> + 567 + 568 <span class="i">$InternalBondStereo</span> = <span class="q">''</span><span class="sc">;</span> + 569 <span class="j">BONDSTEREO:</span> <span class="s">{</span> + 570 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsUp</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 571 <span class="i">$InternalBondStereo</span> = <span class="q">'Up'</span><span class="sc">;</span> + 572 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span> + 573 <span class="s">}</span> + 574 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsDown</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 575 <span class="i">$InternalBondStereo</span> = <span class="q">'Down'</span><span class="sc">;</span> + 576 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span> + 577 <span class="s">}</span> + 578 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsUpOrDown</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 579 <span class="i">$InternalBondStereo</span> = <span class="q">'UpOrDown'</span><span class="sc">;</span> + 580 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span> + 581 <span class="s">}</span> + 582 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsCisOrTrans</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">->IsCis</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">->IsTrans</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 583 <span class="i">$InternalBondStereo</span> = <span class="q">'CisOrTrans'</span><span class="sc">;</span> + 584 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span> + 585 <span class="s">}</span> + 586 <span class="i">$InternalBondStereo</span> = <span class="q">''</span><span class="sc">;</span> + 587 <span class="s">}</span> + 588 + 589 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span> <span class="s">{</span> + 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> + 591 <span class="s">}</span> + 592 + 593 <span class="k">return</span> <span class="i">$BondStereo</span><span class="sc">;</span> + 594 <span class="s">}</span> + 595 + 596 <span class="c"># Zero out charge and radical values specified for atoms...</span> +<a name="_ZeroOutAtomsChargeAndRadicalValues-"></a> 597 <span class="k">sub </span><span class="m">_ZeroOutAtomsChargeAndRadicalValues</span> <span class="s">{</span> + 598 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 599 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> + 600 + 601 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="k">values</span> <span class="i">%</span>{<span class="i">$AtomNumToAtomMapRef</span>}<span class="s">)</span> <span class="s">{</span> + 602 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 603 <span class="i">$Atom</span><span class="i">->DeleteProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="sc">;</span> + 604 <span class="s">}</span> + 605 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 606 <span class="i">$Atom</span><span class="i">->DeleteProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span> + 607 <span class="s">}</span> + 608 <span class="s">}</span> + 609 <span class="s">}</span> + 610 + 611 <span class="c"># Process charge property value pairs...</span> +<a name="_ProcessChargeProperty-"></a> 612 <span class="k">sub </span><span class="m">_ProcessChargeProperty</span> <span class="s">{</span> + 613 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 614 + 615 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 616 <span class="k">return</span><span class="sc">;</span> + 617 <span class="s">}</span> + 618 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 619 + 620 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span> + 621 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 622 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$Charge</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> + 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span> + 624 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> + 625 <span class="s">}</span> + 626 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span> + 627 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> + 628 <span class="s">}</span> + 629 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span> + 630 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 631 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessChargeProperty: Setting formal charge on atom number, $AtomNum, with already assigned spin multiplicity value..."</span><span class="sc">;</span> + 632 <span class="s">}</span> + 633 <span class="i">$Atom</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span> + 634 <span class="s">}</span> + 635 <span class="s">}</span> + 636 + 637 <span class="c"># Get charge property value for an atom...</span> +<a name="_GetChargePropertyValue-"></a> 638 <span class="k">sub </span><span class="m">_GetChargePropertyValue</span> <span class="s">{</span> + 639 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 640 <span class="k">my</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span> + 641 + 642 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span> + 643 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 644 <span class="i">$Charge</span> = <span class="i">$Atom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 645 <span class="s">}</span> + 646 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span> + 647 <span class="s">}</span> + 648 + 649 <span class="c"># Process charge property value pairs...</span> +<a name="_ProcessRadicalProperty-"></a> 650 <span class="k">sub </span><span class="m">_ProcessRadicalProperty</span> <span class="s">{</span> + 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> + 652 + 653 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 654 <span class="k">return</span><span class="sc">;</span> + 655 <span class="s">}</span> + 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> + 657 + 658 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span> + 659 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 660 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$Radical</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> + 661 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Radical</span><span class="s">)</span> <span class="s">{</span> + 662 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> + 663 <span class="s">}</span> + 664 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span> + 665 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> + 666 <span class="s">}</span> + 667 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span> + 668 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 669 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessRadicalProperty: Setting spin multiplicity on atom number, $AtomNum, with already assigned formal charge value..."</span><span class="sc">;</span> + 670 <span class="s">}</span> + 671 <span class="i">$SpinMultiplicity</span> = <span class="i">SDFileUtil::MDLRadicalToInternalSpinMultiplicity</span><span class="s">(</span><span class="i">$Radical</span><span class="s">)</span><span class="sc">;</span> + 672 <span class="i">$Atom</span><span class="i">->SetSpinMultiplicity</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span> + 673 <span class="s">}</span> + 674 <span class="s">}</span> + 675 + 676 <span class="c"># Get radical property value for an atom...</span> +<a name="_GetRadicalPropertyValue-"></a> 677 <span class="k">sub </span><span class="m">_GetRadicalPropertyValue</span> <span class="s">{</span> + 678 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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> + 680 + 681 <span class="i">$Radical</span> = <span class="n">0</span><span class="sc">;</span> + 682 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 683 <span class="i">$SpinMultiplicity</span> = <span class="i">$Atom</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 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> + 685 <span class="s">}</span> + 686 <span class="k">return</span> <span class="i">$Radical</span><span class="sc">;</span> + 687 <span class="s">}</span> + 688 + 689 <span class="c"># Process isotope property value pairs...</span> +<a name="_ProcessIsotopeProperty-"></a> 690 <span class="k">sub </span><span class="m">_ProcessIsotopeProperty</span> <span class="s">{</span> + 691 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 692 + 693 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 694 <span class="k">return</span><span class="sc">;</span> + 695 <span class="s">}</span> + 696 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> + 697 + 698 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span> + 699 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 700 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$MassNumber</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> + 701 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MassNumber</span><span class="s">)</span> <span class="s">{</span> + 702 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> + 703 <span class="s">}</span> + 704 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span> + 705 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> + 706 <span class="s">}</span> + 707 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span> + 708 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 709 + 710 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 711 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 712 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessProcessIsotopeProperty: Unknown mass number, $MassNumber, specified on M ISO property line for atom number, $AtomNum, in SD for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. The mass number value has been assigned. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...\n"</span><span class="sc">;</span> + 713 <span class="s">}</span> + 714 + 715 <span class="c"># Use SetProperty method instead of SetMassNumber to skip explicit checks on MassNumber value...</span> + 716 <span class="i">$Atom</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span> + 717 <span class="s">}</span> + 718 <span class="s">}</span> + 719 + 720 <span class="c"># Get isotope property value for an atom...</span> +<a name="_GetIsotopePropertyValue-"></a> 721 <span class="k">sub </span><span class="m">_GetIsotopePropertyValue</span> <span class="s">{</span> + 722 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 723 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span> + 724 + 725 <span class="i">$MassNumber</span> = <span class="n">0</span><span class="sc">;</span> + 726 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 727 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 728 <span class="s">}</span> + 729 <span class="k">return</span> <span class="i">$MassNumber</span><span class="sc">;</span> + 730 <span class="s">}</span> + 731 + 732 <span class="c"># Process atom alias property value pairs...</span> +<a name="_ProcessAtomAliasProperty-"></a> 733 <span class="k">sub </span><span class="m">_ProcessAtomAliasProperty</span> <span class="s">{</span> + 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> + 735 + 736 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 737 <span class="k">return</span><span class="sc">;</span> + 738 <span class="s">}</span> + 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">$Atom</span><span class="s">)</span><span class="sc">;</span> + 740 + 741 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span> + 742 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 743 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$AtomAlias</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> + 744 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomNum</span><span class="s">)</span> <span class="s">{</span> + 745 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> + 746 <span class="s">}</span> + 747 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span> + 748 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> + 749 <span class="s">}</span> + 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> + 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> + 752 <span class="i">carp</span><span class="s">(</span><span class="q">"Warning: ${ClassName}->_ProcessAtomAliasProperty: Ignoring atom alias property line: No Atom alias value specified..."</span><span class="s">)</span><span class="sc">;</span> + 753 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> + 754 <span class="s">}</span> + 755 + 756 <span class="c"># Set atom symbol to atom alias which sets atomic number automatically...</span> + 757 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span> + 758 <span class="i">$Atom</span><span class="i">->SetAtomSymbol</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span> + 759 + 760 <span class="i">$Atom</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'AtomAlias'</span><span class="cm">,</span> <span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span> + 761 <span class="s">}</span> + 762 <span class="s">}</span> + 763 + 764 <span class="c"># Get atom alias property value for an atom...</span> +<a name="_GetAtomAliasPropertyValue-"></a> 765 <span class="k">sub </span><span class="m">_GetAtomAliasPropertyValue</span> <span class="s">{</span> + 766 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 767 <span class="k">my</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span> + 768 + 769 <span class="i">$AtomAlias</span> = <span class="k">undef</span><span class="sc">;</span> + 770 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'AtomAlias'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 771 <span class="i">$AtomAlias</span> = <span class="i">$Atom</span><span class="i">->GetAtomAlias</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 772 <span class="s">}</span> + 773 <span class="k">return</span> <span class="i">$AtomAlias</span><span class="sc">;</span> + 774 <span class="s">}</span> + 775 + 776 <span class="c"># Is it a MDLMolFileIO object?</span> +<a name="_IsMDLMolFileIO-"></a> 777 <span class="k">sub </span><span class="m">_IsMDLMolFileIO</span> <span class="s">{</span> + 778 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 779 + 780 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 781 <span class="s">}</span> + 782 + 783 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>