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comparison mayachemtools/docs/modules/html/code/MDLMolFileIO.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:FileIO::MDLMolFileIO.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-FileIO::MDLMolFileIO-"></a> 1 <span class="k">package </span><span class="i">FileIO::MDLMolFileIO</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: MDLMolFileIO.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:48:43 $</span> | |
| 18 5 <span class="c"># $Revision: 1.32 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">SDFileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">FileIO::FileIO</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
| 51 38 | |
| 52 39 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> | |
| 53 40 | |
| 54 41 <span class="i">@ISA</span> = <span class="q">qw(FileIO::FileIO Exporter)</span><span class="sc">;</span> | |
| 55 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 56 43 <span class="i">@EXPORT_OK</span> = <span class="q">qw(IsMDLMolFile)</span><span class="sc">;</span> | |
| 57 44 | |
| 58 45 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
| 59 46 | |
| 60 47 <span class="c"># Setup class variables...</span> | |
| 61 48 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 62 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 63 50 | |
| 64 51 <span class="c"># Class constructor...</span> | |
| 65 <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 66 53 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 67 54 | |
| 68 55 <span class="c"># Initialize object...</span> | |
| 69 56 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 70 57 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> | |
| 71 58 <span class="i">$This</span><span class="i">->_InitializeMDLMolFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 72 59 | |
| 73 60 <span class="i">$This</span><span class="i">->_InitializeMDLMolFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 74 61 | |
| 75 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 76 63 <span class="s">}</span> | |
| 77 64 | |
| 78 65 <span class="c"># Initialize any local object data...</span> | |
| 79 66 <span class="c">#</span> | |
| 80 <a name="_InitializeMDLMolFileIO-"></a> 67 <span class="k">sub </span><span class="m">_InitializeMDLMolFileIO</span> <span class="s">{</span> | |
| 81 68 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 82 69 | |
| 83 70 <span class="c"># Nothing to do: Base class FileIO handles default class variables...</span> | |
| 84 71 | |
| 85 72 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 86 73 <span class="s">}</span> | |
| 87 74 | |
| 88 75 <span class="c"># Initialize class ...</span> | |
| 89 <a name="_InitializeClass-"></a> 76 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 90 77 <span class="c">#Class name...</span> | |
| 91 78 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 92 79 | |
| 93 80 <span class="s">}</span> | |
| 94 81 | |
| 95 82 <span class="c"># Initialize object values...</span> | |
| 96 <a name="_InitializeMDLMolFileIOProperties-"></a> 83 <span class="k">sub </span><span class="m">_InitializeMDLMolFileIOProperties</span> <span class="s">{</span> | |
| 97 84 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 98 85 | |
| 99 86 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> | |
| 100 87 <span class="c"># are implemented on-demand using ObjectProperty class.</span> | |
| 101 88 | |
| 102 89 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
| 103 90 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 104 91 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 105 92 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 106 93 <span class="s">}</span> | |
| 107 94 | |
| 108 95 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="s">)</span> <span class="s">{</span> | |
| 109 96 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying file name..."</span><span class="sc">;</span> | |
| 110 97 <span class="s">}</span> | |
| 111 98 | |
| 112 99 <span class="c"># Make sure it's a MDLMol file...</span> | |
| 113 100 <span class="i">$Name</span> = <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="sc">;</span> | |
| 114 101 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsMDLMolFile</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 115 102 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $Name, doesn't appear to be MDLMol format..."</span><span class="sc">;</span> | |
| 116 103 <span class="s">}</span> | |
| 117 104 | |
| 118 105 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 119 106 <span class="s">}</span> | |
| 120 107 | |
| 121 108 <span class="c"># Is it a MDLMol file?</span> | |
| 122 <a name="IsMDLMolFile-"></a> 109 <span class="k">sub </span><span class="m">IsMDLMolFile ($;$)</span> <span class="s">{</span> | |
| 123 110 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 124 111 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 125 112 | |
| 126 113 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMDLMolFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 127 114 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FileName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 128 115 <span class="s">}</span> | |
| 129 116 <span class="k">else</span> <span class="s">{</span> | |
| 130 117 <span class="i">$FileName</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> | |
| 131 118 <span class="s">}</span> | |
| 132 119 | |
| 133 120 <span class="c"># Check file extension...</span> | |
| 134 121 <span class="i">$Status</span> = <span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"mol"</span><span class="s">)</span><span class="sc">;</span> | |
| 135 122 | |
| 136 123 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 137 124 <span class="s">}</span> | |
| 138 125 | |
| 139 126 <span class="c"># Read molecule from file and return molecule object...</span> | |
| 140 <a name="ReadMolecule-"></a> 127 <span class="k">sub </span><span class="m">ReadMolecule</span> <span class="s">{</span> | |
| 141 128 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 142 129 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> | |
| 143 130 | |
| 144 131 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 145 132 <span class="k">return</span> <span class="i">$This</span><span class="i">->ParseMoleculeString</span><span class="s">(</span><span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 146 133 <span class="s">}</span> | |
| 147 134 | |
| 148 135 <span class="c"># Write compound data using Molecule object...</span> | |
| 149 <a name="WriteMolecule-"></a> 136 <span class="k">sub </span><span class="m">WriteMolecule</span> <span class="s">{</span> | |
| 150 137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 151 138 | |
| 152 139 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> && <span class="i">$Molecule</span><span class="i">->IsMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 153 140 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->WriteMolecule: No data written: Molecule object is not specified..."</span><span class="sc">;</span> | |
| 154 141 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 155 142 <span class="s">}</span> | |
| 156 143 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> | |
| 157 144 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 158 145 | |
| 159 146 <span class="k">print</span> <span class="i">$FileHandle</span> <span class="i">$This</span><span class="i">->GenerateMoleculeString</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> . <span class="q">"\n"</span><span class="sc">;</span> | |
| 160 147 | |
| 161 148 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 162 149 <span class="s">}</span> | |
| 163 150 | |
| 164 151 <span class="c"># Retrieve molecule string...</span> | |
| 165 <a name="ReadMoleculeString-"></a> 152 <span class="k">sub </span><span class="m">ReadMoleculeString</span> <span class="s">{</span> | |
| 166 153 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 167 154 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> | |
| 168 155 | |
| 169 156 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 170 157 <span class="k">return</span> <span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> | |
| 171 158 <span class="s">}</span> | |
| 172 159 | |
| 173 160 <span class="c"># Parse molecule string and return molecule object. ParseMoleculeString supports two invocation methods: class</span> | |
| 174 161 <span class="c"># method or a package function.</span> | |
| 175 162 <span class="c">#</span> | |
| 176 <a name="ParseMoleculeString-"></a> 163 <span class="k">sub </span><span class="m">ParseMoleculeString</span> <span class="s">{</span> | |
| 177 164 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 178 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="s">)</span><span class="sc">;</span> | |
| 179 166 | |
| 180 167 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMDLMolFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 181 168 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 182 169 <span class="s">}</span> | |
| 183 170 <span class="k">else</span> <span class="s">{</span> | |
| 184 171 <span class="i">$MoleculeString</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> | |
| 185 172 <span class="i">$This</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 186 173 <span class="s">}</span> | |
| 187 174 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MoleculeString</span><span class="s">)</span> <span class="s">{</span> | |
| 188 175 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 189 176 <span class="s">}</span> | |
| 190 177 <span class="k">my</span><span class="s">(</span><span class="i">$LineIndex</span><span class="cm">,</span> <span class="i">@MoleculeLines</span><span class="s">)</span><span class="sc">;</span> | |
| 191 178 <span class="i">@MoleculeLines</span> = <span class="k">split</span> <span class="q">/\n/</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="sc">;</span> | |
| 192 179 | |
| 193 180 <span class="c"># Create molecule object and set molecule level native and MDL properties...</span> | |
| 194 181 <span class="c">#</span> | |
| 195 182 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 196 183 <span class="i">$Molecule</span> = <span class="i">new</span> <span class="i">Molecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 197 184 | |
| 198 185 <span class="c"># Set valence model for calculating implicit hydrogens...</span> | |
| 199 186 <span class="i">$Molecule</span><span class="i">->SetValenceModel</span><span class="s">(</span><span class="q">'MDLValenceModel'</span><span class="s">)</span><span class="sc">;</span> | |
| 200 187 | |
| 201 188 <span class="c"># Process headers data...</span> | |
| 202 189 <span class="i">$LineIndex</span> = <span class="n">0</span><span class="sc">;</span> | |
| 203 190 <span class="k">my</span><span class="s">(</span><span class="i">$MoleculeName</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdMolNameLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span> | |
| 204 191 <span class="i">$MoleculeName</span> = <span class="i">TextUtil::RemoveTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$MoleculeName</span><span class="s">)</span><span class="sc">;</span> | |
| 205 192 <span class="i">$Molecule</span><span class="i">->SetName</span><span class="s">(</span><span class="i">$MoleculeName</span><span class="s">)</span><span class="sc">;</span> | |
| 206 193 | |
| 207 194 <span class="i">$LineIndex</span>++<span class="sc">;</span> | |
| 208 195 <span class="k">my</span><span class="s">(</span><span class="i">$UserInitial</span><span class="cm">,</span> <span class="i">$ProgramName</span><span class="cm">,</span> <span class="i">$Date</span><span class="cm">,</span> <span class="i">$Code</span><span class="cm">,</span> <span class="i">$ScalingFactor1</span><span class="cm">,</span> <span class="i">$ScalingFactor2</span><span class="cm">,</span> <span class="i">$Energy</span><span class="cm">,</span> <span class="i">$RegistryNum</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdMiscInfoLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span> | |
| 209 196 <span class="i">$Molecule</span><span class="i">->SetProperties</span><span class="s">(</span><span class="q">'MDLUserInitial'</span> <span class="cm">=></span> <span class="i">$UserInitial</span><span class="cm">,</span> <span class="q">'MDLProgramName'</span> <span class="cm">=></span> <span class="i">$ProgramName</span><span class="cm">,</span> <span class="q">'MDLDate'</span> <span class="cm">=></span> <span class="i">$Date</span><span class="cm">,</span> <span class="q">'MDLCode'</span> <span class="cm">=></span> <span class="i">$Code</span><span class="cm">,</span> <span class="q">'MDLScalingFactor1'</span> <span class="cm">=></span> <span class="i">$ScalingFactor1</span><span class="cm">,</span> <span class="q">'MDLScalingFactor2'</span> <span class="cm">=></span> <span class="i">$ScalingFactor2</span><span class="cm">,</span> <span class="q">'MDLEnergy'</span> <span class="cm">=></span> <span class="i">$Energy</span><span class="cm">,</span> <span class="q">'MDLRegistryNum'</span> <span class="cm">=></span> <span class="i">$RegistryNum</span><span class="s">)</span><span class="sc">;</span> | |
| 210 197 | |
| 211 198 <span class="i">$LineIndex</span>++<span class="sc">;</span> | |
| 212 199 <span class="k">my</span><span class="s">(</span><span class="i">$Comments</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdCommentsLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span> | |
| 213 200 <span class="i">$Molecule</span><span class="i">->SetProperties</span><span class="s">(</span><span class="q">'MDLComments'</span> <span class="cm">=></span> <span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span> | |
| 214 201 | |
| 215 202 <span class="i">$LineIndex</span>++<span class="sc">;</span> | |
| 216 203 <span class="k">my</span><span class="s">(</span><span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$BondCount</span><span class="cm">,</span> <span class="i">$ChiralFlag</span><span class="cm">,</span> <span class="i">$PropertyCount</span><span class="cm">,</span> <span class="i">$Version</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdCountsLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span> | |
| 217 204 | |
| 218 205 <span class="i">$Molecule</span><span class="i">->SetProperties</span><span class="s">(</span><span class="q">'MDLChiralFlag'</span> <span class="cm">=></span> <span class="i">$ChiralFlag</span><span class="cm">,</span> <span class="q">'MDLPropertyCount'</span> <span class="cm">=></span> <span class="i">$PropertyCount</span><span class="cm">,</span> <span class="q">'MDLVersion'</span> <span class="cm">=></span> <span class="i">$Version</span><span class="s">)</span><span class="sc">;</span> | |
| 219 206 | |
| 220 207 <span class="c"># Process atom data...</span> | |
| 221 208 <span class="k">my</span><span class="s">(</span><span class="i">$FirstAtomLineIndex</span><span class="cm">,</span> <span class="i">$LastAtomLineIndex</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> | |
| 222 209 | |
| 223 210 <span class="i">$AtomNum</span> = <span class="n">0</span><span class="sc">;</span> | |
| 224 211 <span class="i">%AtomNumToAtomMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 225 212 <span class="i">$FirstAtomLineIndex</span> = <span class="n">4</span><span class="sc">;</span> <span class="i">$LastAtomLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span> - <span class="n">1</span><span class="sc">;</span> | |
| 226 213 | |
| 227 214 <span class="k">for</span> <span class="s">(</span><span class="i">$LineIndex</span> = <span class="i">$FirstAtomLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span> <= <span class="i">$LastAtomLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span>++<span class="s">)</span> <span class="s">{</span> | |
| 228 215 <span class="i">$AtomNum</span>++<span class="sc">;</span> | |
| 229 216 <span class="s">(</span><span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdAtomLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span> | |
| 230 217 | |
| 231 218 <span class="i">$Atom</span> = <span class="i">new</span> <span class="i">Atom</span><span class="s">(</span><span class="q">'AtomSymbol'</span> <span class="cm">=></span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="q">'XYZ'</span> <span class="cm">=></span> <span class="s">[</span><span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
| 232 219 | |
| 233 220 <span class="k">if</span> <span class="s">(</span><span class="i">$MassDifference</span> && <span class="i">$MassDifference</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 234 221 <span class="i">_ProcessMassDifference</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="s">)</span><span class="sc">;</span> | |
| 235 222 <span class="s">}</span> | |
| 236 223 <span class="k">if</span> <span class="s">(</span><span class="i">$Charge</span> && <span class="i">$Charge</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 237 224 <span class="i">_ProcessCharge</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span> | |
| 238 225 <span class="s">}</span> | |
| 239 226 <span class="k">if</span> <span class="s">(</span><span class="i">$StereoParity</span> && <span class="i">$StereoParity</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 240 227 <span class="i">_ProcessStereoParity</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span> | |
| 241 228 <span class="s">}</span> | |
| 242 229 | |
| 243 230 <span class="i">$AtomNumToAtomMap</span>{<span class="i">$AtomNum</span>} = <span class="i">$Atom</span><span class="sc">;</span> | |
| 244 231 <span class="i">$Molecule</span><span class="i">->AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 245 232 <span class="s">}</span> | |
| 246 233 | |
| 247 234 <span class="c"># Process bond data...</span> | |
| 248 235 <span class="k">my</span><span class="s">(</span><span class="i">$FirstBondLineIndex</span><span class="cm">,</span> <span class="i">$LastBondLineIndex</span><span class="cm">,</span> <span class="i">$FirstAtomNum</span><span class="cm">,</span> <span class="i">$SecondAtomNum</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="cm">,</span> <span class="i">$InternalBondOrder</span><span class="cm">,</span> <span class="i">$InternalBondType</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 249 236 | |
| 250 237 <span class="i">$FirstBondLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span><span class="sc">;</span> | |
| 251 238 <span class="i">$LastBondLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span> + <span class="i">$BondCount</span> - <span class="n">1</span><span class="sc">;</span> | |
| 252 239 | |
| 253 240 <span class="k">for</span> <span class="s">(</span><span class="i">$LineIndex</span> = <span class="i">$FirstBondLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span> <= <span class="i">$LastBondLineIndex</span><span class="sc">;</span> <span class="i">$LineIndex</span>++<span class="s">)</span> <span class="s">{</span> | |
| 254 241 <span class="s">(</span><span class="i">$FirstAtomNum</span><span class="cm">,</span> <span class="i">$SecondAtomNum</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span> = <span class="i">SDFileUtil::ParseCmpdBondLine</span><span class="s">(</span><span class="i">$MoleculeLines</span>[<span class="i">$LineIndex</span>]<span class="s">)</span><span class="sc">;</span> | |
| 255 242 | |
| 256 243 <span class="i">$Atom1</span> = <span class="i">$AtomNumToAtomMap</span>{<span class="i">$FirstAtomNum</span>}<span class="sc">;</span> | |
| 257 244 <span class="i">$Atom2</span> = <span class="i">$AtomNumToAtomMap</span>{<span class="i">$SecondAtomNum</span>}<span class="sc">;</span> | |
| 258 245 | |
| 259 246 <span class="s">(</span><span class="i">$InternalBondOrder</span><span class="cm">,</span> <span class="i">$InternalBondType</span><span class="s">)</span> = <span class="i">SDFileUtil::MDLBondTypeToInternalBondOrder</span><span class="s">(</span><span class="i">$BondType</span><span class="s">)</span><span class="sc">;</span> | |
| 260 247 <span class="i">$Bond</span> = <span class="i">new</span> <span class="i">Bond</span><span class="s">(</span><span class="q">'Atoms'</span> <span class="cm">=></span> <span class="s">[</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">]</span><span class="cm">,</span> <span class="q">'BondOrder'</span> <span class="cm">=></span> <span class="i">$InternalBondOrder</span><span class="s">)</span><span class="sc">;</span> | |
| 261 248 <span class="i">$Bond</span><span class="i">->SetBondType</span><span class="s">(</span><span class="i">$InternalBondType</span><span class="s">)</span><span class="sc">;</span> | |
| 262 249 | |
| 263 250 <span class="k">if</span> <span class="s">(</span><span class="i">$BondStereo</span> && <span class="i">$BondStereo</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 264 251 <span class="i">_ProcessBondStereo</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span><span class="sc">;</span> | |
| 265 252 <span class="s">}</span> | |
| 266 253 | |
| 267 254 <span class="i">$Molecule</span><span class="i">->AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 268 255 <span class="s">}</span> | |
| 269 256 | |
| 270 257 <span class="c"># Process available property block lines starting with A aaa, M CHG, M ISO and M RAD. All other property blocks</span> | |
| 271 258 <span class="c"># lines are for query or specific display purposes and are ignored for now.</span> | |
| 272 259 <span class="c">#</span> | |
| 273 260 <span class="c">#</span> | |
| 274 261 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyLineIndex</span><span class="cm">,</span> <span class="i">$PropertyLine</span><span class="cm">,</span> <span class="i">$FirstChargeOrRadicalLine</span><span class="cm">,</span> <span class="i">@ValuePairs</span><span class="s">)</span><span class="sc">;</span> | |
| 275 262 | |
| 276 263 <span class="i">$PropertyLineIndex</span> = <span class="i">$FirstAtomLineIndex</span> + <span class="i">$AtomCount</span> + <span class="i">$BondCount</span><span class="sc">;</span> | |
| 277 264 <span class="i">$PropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span> | |
| 278 265 <span class="i">$FirstChargeOrRadicalLine</span> = <span class="n">1</span><span class="sc">;</span> | |
| 279 266 | |
| 280 267 <span class="j">PROPERTYLINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$PropertyLine</span> !~ <span class="q">/^M END/i</span> <span class="s">)</span> <span class="s">{</span> | |
| 281 268 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span> | |
| 282 269 <span class="k">last</span> <span class="j">PROPERTYLINE</span><span class="sc">;</span> | |
| 283 270 <span class="s">}</span> | |
| 284 271 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^(M CHG|M RAD)/i</span><span class="s">)</span> <span class="s">{</span> | |
| 285 272 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstChargeOrRadicalLine</span><span class="s">)</span> <span class="s">{</span> | |
| 286 273 <span class="i">$FirstChargeOrRadicalLine</span> = <span class="n">0</span><span class="sc">;</span> | |
| 287 274 <span class="i">_ZeroOutAtomsChargeAndRadicalValues</span><span class="s">(</span>\<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> | |
| 288 275 <span class="s">}</span> | |
| 289 276 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M CHG/i</span><span class="s">)</span> <span class="s">{</span> | |
| 290 277 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdChargePropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span> | |
| 291 278 <span class="i">_ProcessChargeProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> | |
| 292 279 <span class="s">}</span> | |
| 293 280 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M RAD/i</span><span class="s">)</span> <span class="s">{</span> | |
| 294 281 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdRadicalPropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span> | |
| 295 282 <span class="i">_ProcessRadicalProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> | |
| 296 283 <span class="s">}</span> | |
| 297 284 <span class="s">}</span> | |
| 298 285 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^M ISO/i</span><span class="s">)</span> <span class="s">{</span> | |
| 299 286 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdIsotopePropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="s">)</span><span class="sc">;</span> | |
| 300 287 <span class="i">_ProcessIsotopeProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> | |
| 301 288 <span class="s">}</span> | |
| 302 289 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PropertyLine</span> =~ <span class="q">/^A /i</span><span class="s">)</span> <span class="s">{</span> | |
| 303 290 <span class="k">my</span><span class="s">(</span><span class="i">$NextPropertyLine</span><span class="s">)</span><span class="sc">;</span> | |
| 304 291 <span class="i">$PropertyLineIndex</span>++<span class="sc">;</span> | |
| 305 292 <span class="i">$NextPropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span> | |
| 306 293 <span class="i">@ValuePairs</span> = <span class="i">SDFileUtil::ParseCmpdAtomAliasPropertyLine</span><span class="s">(</span><span class="i">$PropertyLine</span><span class="cm">,</span> <span class="i">$NextPropertyLine</span><span class="s">)</span><span class="sc">;</span> | |
| 307 294 <span class="i">_ProcessAtomAliasProperty</span><span class="s">(</span>\<span class="i">@ValuePairs</span><span class="cm">,</span> \<span class="i">%AtomNumToAtomMap</span><span class="s">)</span><span class="sc">;</span> | |
| 308 295 <span class="s">}</span> | |
| 309 296 <span class="i">$PropertyLineIndex</span>++<span class="sc">;</span> | |
| 310 297 <span class="i">$PropertyLine</span> = <span class="i">$MoleculeLines</span>[<span class="i">$PropertyLineIndex</span>]<span class="sc">;</span> | |
| 311 298 <span class="s">}</span> | |
| 312 299 <span class="c"># Store input molecule string as generic property of molecule...</span> | |
| 313 300 <span class="i">$Molecule</span><span class="i">->SetInputMoleculeString</span><span class="s">(</span><span class="i">$MoleculeString</span><span class="s">)</span><span class="sc">;</span> | |
| 314 301 | |
| 315 302 <span class="k">return</span> <span class="i">$Molecule</span><span class="sc">;</span> | |
| 316 303 <span class="s">}</span> | |
| 317 304 | |
| 318 305 <span class="c"># Generate molecule string using molecule object...</span> | |
| 319 <a name="GenerateMoleculeString-"></a> 306 <span class="k">sub </span><span class="m">GenerateMoleculeString</span> <span class="s">{</span> | |
| 320 307 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 321 308 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 322 309 | |
| 323 310 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMDLMolFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 324 311 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 325 312 <span class="s">}</span> | |
| 326 313 <span class="k">else</span> <span class="s">{</span> | |
| 327 314 <span class="i">$Molecule</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> | |
| 328 315 <span class="i">$This</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 329 316 <span class="s">}</span> | |
| 330 317 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 331 318 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 332 319 <span class="s">}</span> | |
| 333 320 <span class="k">my</span><span class="s">(</span><span class="i">@MoleculeLines</span><span class="s">)</span><span class="sc">;</span> | |
| 334 321 <span class="i">@MoleculeLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 335 322 | |
| 336 323 <span class="c"># First line: Molname line...</span> | |
| 337 324 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdMolNameLine</span><span class="s">(</span><span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 338 325 | |
| 339 326 <span class="c"># Second line: Misc info...</span> | |
| 340 327 <span class="k">my</span><span class="s">(</span><span class="i">$ProgramName</span><span class="cm">,</span> <span class="i">$UserInitial</span><span class="cm">,</span> <span class="i">$Code</span><span class="s">)</span><span class="sc">;</span> | |
| 341 328 <span class="i">$ProgramName</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$UserInitial</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$Code</span> = <span class="q">''</span><span class="sc">;</span> | |
| 342 329 | |
| 343 330 <span class="i">$Code</span> = <span class="i">$Molecule</span><span class="i">->IsThreeDimensional</span><span class="s">(</span><span class="s">)</span> ? <span class="q">'3D'</span> <span class="co">:</span> <span class="q">'2D'</span><span class="sc">;</span> | |
| 344 331 | |
| 345 332 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdMiscInfoLine</span><span class="s">(</span><span class="i">$ProgramName</span><span class="cm">,</span> <span class="i">$UserInitial</span><span class="cm">,</span> <span class="i">$Code</span><span class="s">)</span><span class="sc">;</span> | |
| 346 333 | |
| 347 334 <span class="c"># Third line: Comments line...</span> | |
| 348 335 <span class="k">my</span><span class="s">(</span><span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span> | |
| 349 336 <span class="i">$Comments</span> = <span class="i">$Molecule</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MDLComments'</span><span class="s">)</span> ? <span class="i">$Molecule</span><span class="i">->GetMDLComments</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Comments'</span><span class="s">)</span> ? <span class="i">$Molecule</span><span class="i">->GetComments</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span> | |
| 350 337 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdCommentsLine</span><span class="s">(</span><span class="i">$Comments</span><span class="s">)</span><span class="sc">;</span> | |
| 351 338 | |
| 352 339 <span class="c"># Fourth line: Counts line for V2000</span> | |
| 353 340 <span class="k">my</span><span class="s">(</span><span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$BondCount</span><span class="cm">,</span> <span class="i">$ChiralFlag</span><span class="s">)</span><span class="sc">;</span> | |
| 354 341 <span class="i">$AtomCount</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 355 342 <span class="i">$BondCount</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 356 343 <span class="i">$ChiralFlag</span> = <span class="n">0</span><span class="sc">;</span> | |
| 357 344 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdCountsLine</span><span class="s">(</span><span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$BondCount</span><span class="cm">,</span> <span class="i">$ChiralFlag</span><span class="s">)</span><span class="sc">;</span> | |
| 358 345 | |
| 359 346 <span class="c"># Atom lines...</span> | |
| 360 347 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">%AtomIDToNum</span><span class="s">)</span><span class="sc">;</span> | |
| 361 348 <span class="k">my</span><span class="s">(</span><span class="i">$ChargePropertyValue</span><span class="cm">,</span> <span class="i">$IsotopePropertyValue</span><span class="cm">,</span> <span class="i">$RadicalPropertyValue</span><span class="cm">,</span> <span class="i">$AtomAliasPropertyValue</span><span class="cm">,</span> <span class="i">@IsotopePropertyValuePairs</span><span class="cm">,</span> <span class="i">@ChargePropertyValuePairs</span><span class="cm">,</span> <span class="i">@RadicalPropertyValuePairs</span><span class="cm">,</span> <span class="i">@AtomAliasPropertyValuePairs</span><span class="s">)</span><span class="sc">;</span> | |
| 362 349 | |
| 363 350 <span class="i">@ChargePropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 364 351 <span class="i">@IsotopePropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 365 352 <span class="i">@RadicalPropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 366 353 <span class="i">@AtomAliasPropertyValuePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 367 354 | |
| 368 355 <span class="i">@Atoms</span> = <span class="i">$Molecule</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 369 356 | |
| 370 357 <span class="i">$AtomNum</span> = <span class="n">0</span><span class="sc">;</span> | |
| 371 358 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 372 359 <span class="i">$AtomNum</span>++<span class="sc">;</span> | |
| 373 360 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 374 361 <span class="i">$AtomIDToNum</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomNum</span><span class="sc">;</span> | |
| 375 362 | |
| 376 363 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 377 364 <span class="s">(</span><span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="s">)</span> = <span class="i">$Atom</span><span class="i">->GetXYZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 378 365 | |
| 379 366 <span class="c"># Setup mass difference...</span> | |
| 380 367 <span class="i">$MassDifference</span> = <span class="i">_GetMassDifference</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 381 368 <span class="k">if</span> <span class="s">(</span><span class="i">$MassDifference</span><span class="s">)</span> <span class="s">{</span> | |
| 382 369 <span class="c"># Hold it for M ISO property lines...</span> | |
| 383 370 <span class="i">$IsotopePropertyValue</span> = <span class="i">_GetIsotopePropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 384 371 <span class="k">if</span> <span class="s">(</span><span class="i">$IsotopePropertyValue</span><span class="s">)</span> <span class="s">{</span> | |
| 385 372 <span class="k">push</span> <span class="i">@IsotopePropertyValuePairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$IsotopePropertyValue</span><span class="s">)</span><span class="sc">;</span> | |
| 386 373 <span class="s">}</span> | |
| 387 374 <span class="s">}</span> | |
| 388 375 | |
| 389 376 <span class="c"># Setup charge...</span> | |
| 390 377 <span class="i">$Charge</span> = <span class="i">_GetCharge</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 391 378 <span class="k">if</span> <span class="s">(</span><span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span> | |
| 392 379 <span class="c"># Hold it for M CHG property lines...</span> | |
| 393 380 <span class="i">$ChargePropertyValue</span> = <span class="i">_GetChargePropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 394 381 <span class="k">if</span> <span class="s">(</span><span class="i">$ChargePropertyValue</span><span class="s">)</span> <span class="s">{</span> | |
| 395 382 <span class="k">push</span> <span class="i">@ChargePropertyValuePairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$ChargePropertyValue</span><span class="s">)</span><span class="sc">;</span> | |
| 396 383 <span class="s">}</span> | |
| 397 384 <span class="s">}</span> | |
| 398 385 | |
| 399 386 <span class="c"># Hold any radical values for for M RAD property lines...</span> | |
| 400 387 <span class="i">$RadicalPropertyValue</span> = <span class="i">_GetRadicalPropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 401 388 <span class="k">if</span> <span class="s">(</span><span class="i">$RadicalPropertyValue</span><span class="s">)</span> <span class="s">{</span> | |
| 402 389 <span class="k">push</span> <span class="i">@RadicalPropertyValuePairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$RadicalPropertyValue</span><span class="s">)</span><span class="sc">;</span> | |
| 403 390 <span class="s">}</span> | |
| 404 391 | |
| 405 392 <span class="c"># Hold any atom alias value for A xxx property lines....</span> | |
| 406 393 <span class="i">$AtomAliasPropertyValue</span> = <span class="i">_GetAtomAliasPropertyValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 407 394 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomAliasPropertyValue</span><span class="s">)</span> <span class="s">{</span> | |
| 408 395 <span class="k">push</span> <span class="i">@AtomAliasPropertyValuePairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$AtomAliasPropertyValue</span><span class="s">)</span><span class="sc">;</span> | |
| 409 396 | |
| 410 397 <span class="c"># Set AtomSymbol to carbon as atom alias would override its value during parsing...</span> | |
| 411 398 <span class="i">$AtomSymbol</span> = <span class="q">"C"</span><span class="sc">;</span> | |
| 412 399 <span class="s">}</span> | |
| 413 400 | |
| 414 401 <span class="c"># Setup stereo parity...</span> | |
| 415 402 <span class="i">$StereoParity</span> = <span class="i">_GetStereoParity</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 416 403 | |
| 417 404 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdAtomLine</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomX</span><span class="cm">,</span> <span class="i">$AtomY</span><span class="cm">,</span> <span class="i">$AtomZ</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span> | |
| 418 405 <span class="s">}</span> | |
| 419 406 | |
| 420 407 <span class="c"># Bond lines...</span> | |
| 421 408 <span class="k">my</span><span class="s">(</span><span class="i">$FirstAtomID</span><span class="cm">,</span> <span class="i">$FirstAtom</span><span class="cm">,</span> <span class="i">$FirstAtomNum</span><span class="cm">,</span> <span class="i">$SecondAtomID</span><span class="cm">,</span> <span class="i">$SecondAtom</span><span class="cm">,</span> <span class="i">$SecondAtomNum</span><span class="cm">,</span> <span class="i">$MDLBondType</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$MDLBondStereo</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> | |
| 422 409 <span class="k">for</span> <span class="i">$FirstAtom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 423 410 <span class="i">$FirstAtomID</span> = <span class="i">$FirstAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 424 411 <span class="i">$FirstAtomNum</span> = <span class="i">$AtomIDToNum</span>{<span class="i">$FirstAtomID</span>}<span class="sc">;</span> | |
| 425 412 | |
| 426 413 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 427 414 <span class="i">@Bonds</span> = <span class="i">$FirstAtom</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 428 415 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 429 416 <span class="i">$SecondAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$FirstAtom</span><span class="s">)</span><span class="sc">;</span> | |
| 430 417 <span class="i">$SecondAtomID</span> = <span class="i">$SecondAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 431 418 <span class="i">$SecondAtomNum</span> = <span class="i">$AtomIDToNum</span>{<span class="i">$SecondAtomID</span>}<span class="sc">;</span> | |
| 432 419 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomNum</span> >= <span class="i">$SecondAtomNum</span><span class="s">)</span> <span class="s">{</span> | |
| 433 420 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 434 421 <span class="s">}</span> | |
| 435 422 <span class="c"># Setup BondType...</span> | |
| 436 423 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 437 424 <span class="i">$BondType</span> = <span class="i">$Bond</span><span class="i">->GetBondType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 438 425 <span class="i">$MDLBondType</span> = <span class="i">SDFileUtil::InternalBondOrderToMDLBondType</span><span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$BondType</span><span class="s">)</span><span class="sc">;</span> | |
| 439 426 | |
| 440 427 <span class="c"># Setup BondStereo...</span> | |
| 441 428 <span class="i">$MDLBondStereo</span> = <span class="i">_GetBondStereo</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 442 429 | |
| 443 430 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdBondLine</span><span class="s">(</span><span class="i">$FirstAtomNum</span><span class="cm">,</span> <span class="i">$SecondAtomNum</span><span class="cm">,</span> <span class="i">$MDLBondType</span><span class="cm">,</span> <span class="i">$MDLBondStereo</span><span class="s">)</span><span class="sc">;</span> | |
| 444 431 <span class="s">}</span> | |
| 445 432 <span class="s">}</span> | |
| 446 433 <span class="c"># Property lines...</span> | |
| 447 434 <span class="k">if</span> <span class="s">(</span><span class="i">@IsotopePropertyValuePairs</span><span class="s">)</span> <span class="s">{</span> | |
| 448 435 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdIsotopePropertyLines</span><span class="s">(</span>\<span class="i">@IsotopePropertyValuePairs</span><span class="s">)</span><span class="sc">;</span> | |
| 449 436 <span class="s">}</span> | |
| 450 437 <span class="k">if</span> <span class="s">(</span><span class="i">@ChargePropertyValuePairs</span><span class="s">)</span> <span class="s">{</span> | |
| 451 438 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdChargePropertyLines</span><span class="s">(</span>\<span class="i">@ChargePropertyValuePairs</span><span class="s">)</span><span class="sc">;</span> | |
| 452 439 <span class="s">}</span> | |
| 453 440 <span class="k">if</span> <span class="s">(</span><span class="i">@RadicalPropertyValuePairs</span><span class="s">)</span> <span class="s">{</span> | |
| 454 441 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdRadicalPropertyLines</span><span class="s">(</span>\<span class="i">@RadicalPropertyValuePairs</span><span class="s">)</span><span class="sc">;</span> | |
| 455 442 <span class="s">}</span> | |
| 456 443 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomAliasPropertyValuePairs</span><span class="s">)</span> <span class="s">{</span> | |
| 457 444 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdAtomAliasPropertyLines</span><span class="s">(</span>\<span class="i">@AtomAliasPropertyValuePairs</span><span class="s">)</span><span class="sc">;</span> | |
| 458 445 <span class="s">}</span> | |
| 459 446 | |
| 460 447 <span class="k">push</span> <span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="q">"M END"</span><span class="sc">;</span> | |
| 461 448 | |
| 462 449 <span class="k">return</span> <span class="k">join</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">@MoleculeLines</span><span class="sc">;</span> | |
| 463 450 <span class="s">}</span> | |
| 464 451 | |
| 465 452 <span class="c"># Process MassDifference value and set atom's mass number...</span> | |
| 466 453 <span class="c">#</span> | |
| 467 <a name="_ProcessMassDifference-"></a> 454 <span class="k">sub </span><span class="m">_ProcessMassDifference</span> <span class="s">{</span> | |
| 468 455 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$MassDifference</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 469 456 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="cm">,</span> <span class="i">$NewMassNumber</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 470 457 | |
| 471 458 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 472 459 | |
| 473 460 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 474 461 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessMassDifference: Ignoring specified mass difference value, $MassDifference, in SD file: Assigned to non standard element..."</span><span class="sc">;</span> | |
| 475 462 <span class="k">return</span><span class="sc">;</span> | |
| 476 463 <span class="s">}</span> | |
| 477 464 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 478 465 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MassDifference</span><span class="s">)</span> <span class="s">{</span> | |
| 479 466 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessMassDifference: Ignoring specified mass difference value, $MassDifference, in SD file: Unknown MassNumber value..."</span><span class="sc">;</span> | |
| 480 467 <span class="k">return</span><span class="sc">;</span> | |
| 481 468 <span class="s">}</span> | |
| 482 469 <span class="i">$NewMassNumber</span> = <span class="i">$MassNumber</span> + <span class="i">$MassDifference</span><span class="sc">;</span> | |
| 483 470 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$NewMassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 484 471 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 485 472 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessMassDifference: Unknown mass number, $MassNumber, corresponding to specified mass difference value, $MassDifference, in SD for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. The mass number value has been assigned. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...\n"</span><span class="sc">;</span> | |
| 486 473 <span class="s">}</span> | |
| 487 474 | |
| 488 475 <span class="c"># Use SetProperty method instead of SetMassNumber to skip explicit checks on MassNumber value...</span> | |
| 489 476 <span class="i">$Atom</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="cm">,</span> <span class="i">$NewMassNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 490 477 <span class="s">}</span> | |
| 491 478 | |
| 492 479 <span class="c"># Get mass difference value...</span> | |
| 493 <a name="_GetMassDifference-"></a> 480 <span class="k">sub </span><span class="m">_GetMassDifference</span> <span class="s">{</span> | |
| 494 481 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 495 482 <span class="k">my</span><span class="s">(</span><span class="i">$MassDifference</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="cm">,</span> <span class="i">$MostAbundantMassNumber</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 496 483 | |
| 497 484 <span class="i">$MassDifference</span> = <span class="n">0</span><span class="sc">;</span> | |
| 498 485 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 499 486 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$MassNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 500 487 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 501 488 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 502 489 <span class="i">$MostAbundantMassNumber</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 503 490 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$MostAbundantMassNumber</span><span class="s">)</span> && <span class="i">$MassNumber</span> != <span class="i">$MostAbundantMassNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 504 491 <span class="i">$MassDifference</span> = <span class="i">$MassNumber</span> - <span class="i">$MostAbundantMassNumber</span><span class="sc">;</span> | |
| 505 492 <span class="s">}</span> | |
| 506 493 <span class="s">}</span> | |
| 507 494 <span class="s">}</span> | |
| 508 495 <span class="k">return</span> <span class="i">$MassDifference</span><span class="sc">;</span> | |
| 509 496 <span class="s">}</span> | |
| 510 497 | |
| 511 498 <span class="c"># Process formal charge value and assign it to atom as formal charge...</span> | |
| 512 <a name="_ProcessCharge-"></a> 499 <span class="k">sub </span><span class="m">_ProcessCharge</span> <span class="s">{</span> | |
| 513 500 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$Charge</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 514 501 <span class="k">my</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span> | |
| 515 502 | |
| 516 503 <span class="i">$InternalCharge</span> = <span class="i">SDFileUtil::MDLChargeToInternalCharge</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span> | |
| 517 504 <span class="i">$Atom</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span> | |
| 518 505 <span class="s">}</span> | |
| 519 506 | |
| 520 507 <span class="c"># Get MDL formal charge value ...</span> | |
| 521 <a name="_GetCharge-"></a> 508 <span class="k">sub </span><span class="m">_GetCharge</span> <span class="s">{</span> | |
| 522 509 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 523 510 <span class="k">my</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="cm">,</span> <span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span> | |
| 524 511 | |
| 525 512 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span> | |
| 526 513 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 527 514 <span class="i">$InternalCharge</span> = <span class="i">$Atom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 528 515 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span> <span class="s">{</span> | |
| 529 516 <span class="i">$Charge</span> = <span class="i">SDFileUtil::InternalChargeToMDLCharge</span><span class="s">(</span><span class="i">$InternalCharge</span><span class="s">)</span><span class="sc">;</span> | |
| 530 517 <span class="s">}</span> | |
| 531 518 <span class="s">}</span> | |
| 532 519 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span> | |
| 533 520 <span class="s">}</span> | |
| 534 521 | |
| 535 522 <span class="c"># Process stereo parity value and assign it to atom as MDL property...</span> | |
| 536 523 <span class="c">#</span> | |
| 537 524 <span class="c"># Notes:</span> | |
| 538 525 <span class="c"># . Mark atom as chiral center</span> | |
| 539 526 <span class="c"># . Assign any explicit Clockwise (parity 1), CounterClockwise (parity 2) or either value (parity 3) as property of atom.</span> | |
| 540 527 <span class="c"># . MDL values of Clockwise and CounterClockwise don't correspond to priority assigned to ligands around</span> | |
| 541 528 <span class="c"># stereo center using CIP scheme; consequently, these values can't be used to set internal Stereochemistry for</span> | |
| 542 529 <span class="c"># an atom.</span> | |
| 543 530 <span class="c">#</span> | |
| 544 <a name="_ProcessStereoParity-"></a> 531 <span class="k">sub </span><span class="m">_ProcessStereoParity</span> <span class="s">{</span> | |
| 545 532 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$StereoParity</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 546 533 | |
| 547 534 <span class="i">$Atom</span><span class="i">->SetStereoCenter</span><span class="s">(</span><span class="q">'1'</span><span class="s">)</span><span class="sc">;</span> | |
| 548 535 <span class="i">$Atom</span><span class="i">->SetMDLStereoParity</span><span class="s">(</span><span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span> | |
| 549 536 <span class="s">}</span> | |
| 550 537 | |
| 551 538 <span class="c"># Set stereo parity value to zero for now: The current release of MayaChemTools hasn't implemented</span> | |
| 552 539 <span class="c"># functionality to determine chirality.</span> | |
| 553 540 <span class="c">#</span> | |
| 554 <a name="_GetStereoParity-"></a> 541 <span class="k">sub </span><span class="m">_GetStereoParity</span> <span class="s">{</span> | |
| 555 542 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 556 543 <span class="k">my</span><span class="s">(</span><span class="i">$StereoParity</span><span class="s">)</span><span class="sc">;</span> | |
| 557 544 | |
| 558 545 <span class="i">$StereoParity</span> = <span class="n">0</span><span class="sc">;</span> | |
| 559 546 | |
| 560 547 <span class="k">return</span> <span class="i">$StereoParity</span><span class="sc">;</span> | |
| 561 548 <span class="s">}</span> | |
| 562 549 | |
| 563 550 <span class="c"># Process bond stereo value...</span> | |
| 564 <a name="_ProcessBondStereo-"></a> 551 <span class="k">sub </span><span class="m">_ProcessBondStereo</span> <span class="s">{</span> | |
| 565 552 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 566 553 <span class="k">my</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span><span class="sc">;</span> | |
| 567 554 | |
| 568 555 <span class="i">$InternalBondStereo</span> = <span class="i">SDFileUtil::MDLBondStereoToInternalBondStereochemistry</span><span class="s">(</span><span class="i">$BondStereo</span><span class="s">)</span><span class="sc">;</span> | |
| 569 556 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span> <span class="s">{</span> | |
| 570 557 <span class="i">$Bond</span><span class="i">->SetBondStereochemistry</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span><span class="sc">;</span> | |
| 571 558 <span class="s">}</span> | |
| 572 559 <span class="s">}</span> | |
| 573 560 | |
| 574 561 <span class="c"># Get MDLBondStereo value...</span> | |
| 575 <a name="_GetBondStereo-"></a> 562 <span class="k">sub </span><span class="m">_GetBondStereo</span> <span class="s">{</span> | |
| 576 563 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 577 564 <span class="k">my</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="cm">,</span> <span class="i">$BondStereo</span><span class="s">)</span><span class="sc">;</span> | |
| 578 565 | |
| 579 566 <span class="i">$BondStereo</span> = <span class="n">0</span><span class="sc">;</span> | |
| 580 567 | |
| 581 568 <span class="i">$InternalBondStereo</span> = <span class="q">''</span><span class="sc">;</span> | |
| 582 569 <span class="j">BONDSTEREO:</span> <span class="s">{</span> | |
| 583 570 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsUp</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 584 571 <span class="i">$InternalBondStereo</span> = <span class="q">'Up'</span><span class="sc">;</span> | |
| 585 572 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span> | |
| 586 573 <span class="s">}</span> | |
| 587 574 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsDown</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 588 575 <span class="i">$InternalBondStereo</span> = <span class="q">'Down'</span><span class="sc">;</span> | |
| 589 576 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span> | |
| 590 577 <span class="s">}</span> | |
| 591 578 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsUpOrDown</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 592 579 <span class="i">$InternalBondStereo</span> = <span class="q">'UpOrDown'</span><span class="sc">;</span> | |
| 593 580 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span> | |
| 594 581 <span class="s">}</span> | |
| 595 582 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsCisOrTrans</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">->IsCis</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">->IsTrans</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 596 583 <span class="i">$InternalBondStereo</span> = <span class="q">'CisOrTrans'</span><span class="sc">;</span> | |
| 597 584 <span class="k">last</span> <span class="j">BONDSTEREO</span><span class="sc">;</span> | |
| 598 585 <span class="s">}</span> | |
| 599 586 <span class="i">$InternalBondStereo</span> = <span class="q">''</span><span class="sc">;</span> | |
| 600 587 <span class="s">}</span> | |
| 601 588 | |
| 602 589 <span class="k">if</span> <span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span> <span class="s">{</span> | |
| 603 590 <span class="i">$BondStereo</span> = <span class="i">SDFileUtil::InternalBondStereochemistryToMDLBondStereo</span><span class="s">(</span><span class="i">$InternalBondStereo</span><span class="s">)</span><span class="sc">;</span> | |
| 604 591 <span class="s">}</span> | |
| 605 592 | |
| 606 593 <span class="k">return</span> <span class="i">$BondStereo</span><span class="sc">;</span> | |
| 607 594 <span class="s">}</span> | |
| 608 595 | |
| 609 596 <span class="c"># Zero out charge and radical values specified for atoms...</span> | |
| 610 <a name="_ZeroOutAtomsChargeAndRadicalValues-"></a> 597 <span class="k">sub </span><span class="m">_ZeroOutAtomsChargeAndRadicalValues</span> <span class="s">{</span> | |
| 611 598 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 612 599 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 613 600 | |
| 614 601 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="k">values</span> <span class="i">%</span>{<span class="i">$AtomNumToAtomMapRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 615 602 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 616 603 <span class="i">$Atom</span><span class="i">->DeleteProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="sc">;</span> | |
| 617 604 <span class="s">}</span> | |
| 618 605 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 619 606 <span class="i">$Atom</span><span class="i">->DeleteProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span> | |
| 620 607 <span class="s">}</span> | |
| 621 608 <span class="s">}</span> | |
| 622 609 <span class="s">}</span> | |
| 623 610 | |
| 624 611 <span class="c"># Process charge property value pairs...</span> | |
| 625 <a name="_ProcessChargeProperty-"></a> 612 <span class="k">sub </span><span class="m">_ProcessChargeProperty</span> <span class="s">{</span> | |
| 626 613 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 627 614 | |
| 628 615 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 629 616 <span class="k">return</span><span class="sc">;</span> | |
| 630 617 <span class="s">}</span> | |
| 631 618 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ValuePairsCount</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 632 619 | |
| 633 620 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span> | |
| 634 621 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 635 622 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$Charge</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 636 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span> | |
| 637 624 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> | |
| 638 625 <span class="s">}</span> | |
| 639 626 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span> | |
| 640 627 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> | |
| 641 628 <span class="s">}</span> | |
| 642 629 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span> | |
| 643 630 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 644 631 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessChargeProperty: Setting formal charge on atom number, $AtomNum, with already assigned spin multiplicity value..."</span><span class="sc">;</span> | |
| 645 632 <span class="s">}</span> | |
| 646 633 <span class="i">$Atom</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span> | |
| 647 634 <span class="s">}</span> | |
| 648 635 <span class="s">}</span> | |
| 649 636 | |
| 650 637 <span class="c"># Get charge property value for an atom...</span> | |
| 651 <a name="_GetChargePropertyValue-"></a> 638 <span class="k">sub </span><span class="m">_GetChargePropertyValue</span> <span class="s">{</span> | |
| 652 639 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 653 640 <span class="k">my</span><span class="s">(</span><span class="i">$Charge</span><span class="s">)</span><span class="sc">;</span> | |
| 654 641 | |
| 655 642 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span> | |
| 656 643 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 657 644 <span class="i">$Charge</span> = <span class="i">$Atom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 658 645 <span class="s">}</span> | |
| 659 646 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span> | |
| 660 647 <span class="s">}</span> | |
| 661 648 | |
| 662 649 <span class="c"># Process charge property value pairs...</span> | |
| 663 <a name="_ProcessRadicalProperty-"></a> 650 <span class="k">sub </span><span class="m">_ProcessRadicalProperty</span> <span class="s">{</span> | |
| 664 651 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 665 652 | |
| 666 653 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 667 654 <span class="k">return</span><span class="sc">;</span> | |
| 668 655 <span class="s">}</span> | |
| 669 656 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ValuePairsCount</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$Radical</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 670 657 | |
| 671 658 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span> | |
| 672 659 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 673 660 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$Radical</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 674 661 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Radical</span><span class="s">)</span> <span class="s">{</span> | |
| 675 662 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> | |
| 676 663 <span class="s">}</span> | |
| 677 664 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span> | |
| 678 665 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> | |
| 679 666 <span class="s">}</span> | |
| 680 667 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span> | |
| 681 668 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 682 669 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessRadicalProperty: Setting spin multiplicity on atom number, $AtomNum, with already assigned formal charge value..."</span><span class="sc">;</span> | |
| 683 670 <span class="s">}</span> | |
| 684 671 <span class="i">$SpinMultiplicity</span> = <span class="i">SDFileUtil::MDLRadicalToInternalSpinMultiplicity</span><span class="s">(</span><span class="i">$Radical</span><span class="s">)</span><span class="sc">;</span> | |
| 685 672 <span class="i">$Atom</span><span class="i">->SetSpinMultiplicity</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span> | |
| 686 673 <span class="s">}</span> | |
| 687 674 <span class="s">}</span> | |
| 688 675 | |
| 689 676 <span class="c"># Get radical property value for an atom...</span> | |
| 690 <a name="_GetRadicalPropertyValue-"></a> 677 <span class="k">sub </span><span class="m">_GetRadicalPropertyValue</span> <span class="s">{</span> | |
| 691 678 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 692 679 <span class="k">my</span><span class="s">(</span><span class="i">$Radical</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span> | |
| 693 680 | |
| 694 681 <span class="i">$Radical</span> = <span class="n">0</span><span class="sc">;</span> | |
| 695 682 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 696 683 <span class="i">$SpinMultiplicity</span> = <span class="i">$Atom</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 697 684 <span class="i">$Radical</span> = <span class="i">SDFileUtil::InternalSpinMultiplicityToMDLRadical</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span> | |
| 698 685 <span class="s">}</span> | |
| 699 686 <span class="k">return</span> <span class="i">$Radical</span><span class="sc">;</span> | |
| 700 687 <span class="s">}</span> | |
| 701 688 | |
| 702 689 <span class="c"># Process isotope property value pairs...</span> | |
| 703 <a name="_ProcessIsotopeProperty-"></a> 690 <span class="k">sub </span><span class="m">_ProcessIsotopeProperty</span> <span class="s">{</span> | |
| 704 691 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 705 692 | |
| 706 693 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 707 694 <span class="k">return</span><span class="sc">;</span> | |
| 708 695 <span class="s">}</span> | |
| 709 696 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ValuePairsCount</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 710 697 | |
| 711 698 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span> | |
| 712 699 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 713 700 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$MassNumber</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 714 701 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MassNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 715 702 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> | |
| 716 703 <span class="s">}</span> | |
| 717 704 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span> | |
| 718 705 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> | |
| 719 706 <span class="s">}</span> | |
| 720 707 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span> | |
| 721 708 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 722 709 | |
| 723 710 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 724 711 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 725 712 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessProcessIsotopeProperty: Unknown mass number, $MassNumber, specified on M ISO property line for atom number, $AtomNum, in SD for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. The mass number value has been assigned. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...\n"</span><span class="sc">;</span> | |
| 726 713 <span class="s">}</span> | |
| 727 714 | |
| 728 715 <span class="c"># Use SetProperty method instead of SetMassNumber to skip explicit checks on MassNumber value...</span> | |
| 729 716 <span class="i">$Atom</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 730 717 <span class="s">}</span> | |
| 731 718 <span class="s">}</span> | |
| 732 719 | |
| 733 720 <span class="c"># Get isotope property value for an atom...</span> | |
| 734 <a name="_GetIsotopePropertyValue-"></a> 721 <span class="k">sub </span><span class="m">_GetIsotopePropertyValue</span> <span class="s">{</span> | |
| 735 722 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 736 723 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 737 724 | |
| 738 725 <span class="i">$MassNumber</span> = <span class="n">0</span><span class="sc">;</span> | |
| 739 726 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 740 727 <span class="i">$MassNumber</span> = <span class="i">$Atom</span><span class="i">->GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 741 728 <span class="s">}</span> | |
| 742 729 <span class="k">return</span> <span class="i">$MassNumber</span><span class="sc">;</span> | |
| 743 730 <span class="s">}</span> | |
| 744 731 | |
| 745 732 <span class="c"># Process atom alias property value pairs...</span> | |
| 746 <a name="_ProcessAtomAliasProperty-"></a> 733 <span class="k">sub </span><span class="m">_ProcessAtomAliasProperty</span> <span class="s">{</span> | |
| 747 734 <span class="k">my</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="cm">,</span> <span class="i">$AtomNumToAtomMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 748 735 | |
| 749 736 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuePairsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 750 737 <span class="k">return</span><span class="sc">;</span> | |
| 751 738 <span class="s">}</span> | |
| 752 739 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ValuePairsCount</span><span class="cm">,</span> <span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$AtomAlias</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 753 740 | |
| 754 741 <span class="i">$ValuePairsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ValuePairsRef</span>}<span class="sc">;</span> | |
| 755 742 <span class="j">VALUEPAIRS:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ValuePairsCount</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 756 743 <span class="i">$AtomNum</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$AtomAlias</span> = <span class="i">$ValuePairsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 757 744 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomNum</span><span class="s">)</span> <span class="s">{</span> | |
| 758 745 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> | |
| 759 746 <span class="s">}</span> | |
| 760 747 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="s">)</span> <span class="s">{</span> | |
| 761 748 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> | |
| 762 749 <span class="s">}</span> | |
| 763 750 <span class="i">$AtomAlias</span> = <span class="i">TextUtil::RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span> | |
| 764 751 <span class="k">if</span> <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 765 752 <span class="i">carp</span><span class="s">(</span><span class="q">"Warning: ${ClassName}->_ProcessAtomAliasProperty: Ignoring atom alias property line: No Atom alias value specified..."</span><span class="s">)</span><span class="sc">;</span> | |
| 766 753 <span class="k">next</span> <span class="j">VALUEPAIRS</span><span class="sc">;</span> | |
| 767 754 <span class="s">}</span> | |
| 768 755 | |
| 769 756 <span class="c"># Set atom symbol to atom alias which sets atomic number automatically...</span> | |
| 770 757 <span class="i">$Atom</span> = <span class="i">$AtomNumToAtomMapRef</span>->{<span class="i">$AtomNum</span>}<span class="sc">;</span> | |
| 771 758 <span class="i">$Atom</span><span class="i">->SetAtomSymbol</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span> | |
| 772 759 | |
| 773 760 <span class="i">$Atom</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'AtomAlias'</span><span class="cm">,</span> <span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span> | |
| 774 761 <span class="s">}</span> | |
| 775 762 <span class="s">}</span> | |
| 776 763 | |
| 777 764 <span class="c"># Get atom alias property value for an atom...</span> | |
| 778 <a name="_GetAtomAliasPropertyValue-"></a> 765 <span class="k">sub </span><span class="m">_GetAtomAliasPropertyValue</span> <span class="s">{</span> | |
| 779 766 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 780 767 <span class="k">my</span><span class="s">(</span><span class="i">$AtomAlias</span><span class="s">)</span><span class="sc">;</span> | |
| 781 768 | |
| 782 769 <span class="i">$AtomAlias</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 783 770 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'AtomAlias'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 784 771 <span class="i">$AtomAlias</span> = <span class="i">$Atom</span><span class="i">->GetAtomAlias</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 785 772 <span class="s">}</span> | |
| 786 773 <span class="k">return</span> <span class="i">$AtomAlias</span><span class="sc">;</span> | |
| 787 774 <span class="s">}</span> | |
| 788 775 | |
| 789 776 <span class="c"># Is it a MDLMolFileIO object?</span> | |
| 790 <a name="_IsMDLMolFileIO-"></a> 777 <span class="k">sub </span><span class="m">_IsMDLMolFileIO</span> <span class="s">{</span> | |
| 791 778 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 792 779 | |
| 793 780 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 794 781 <span class="s">}</span> | |
| 795 782 | |
| 796 783 | |
| 797 <a name="EOF-"></a></pre> | |
| 798 <p> </p> | |
| 799 <br /> | |
| 800 <center> | |
| 801 <img src="../../../images/h2o2.png"> | |
| 802 </center> | |
| 803 </body> | |
| 804 </html> |