Mercurial > repos > deepakjadmin > mayatool3_test3
view mayachemtools/docs/modules/html/code/MDLMolFileIO.html @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line source
<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>