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comparison mayachemtools/docs/modules/html/code/SDFileIO.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::SDFileIO.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::SDFileIO-"></a> 1 <span class="k">package </span><span class="i">FileIO::SDFileIO</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: SDFileIO.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:48:43 $</span> | |
| 18 5 <span class="c"># $Revision: 1.35 $</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">FileIO::MDLMolFileIO</span><span class="sc">;</span> | |
| 51 38 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
| 52 39 | |
| 53 40 <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> | |
| 54 41 | |
| 55 42 <span class="i">@ISA</span> = <span class="q">qw(FileIO::FileIO Exporter)</span><span class="sc">;</span> | |
| 56 43 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 57 44 <span class="i">@EXPORT_OK</span> = <span class="q">qw(IsSDFile)</span><span class="sc">;</span> | |
| 58 45 | |
| 59 46 <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> | |
| 60 47 | |
| 61 48 <span class="c"># Setup class variables...</span> | |
| 62 49 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 63 50 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 64 51 | |
| 65 52 <span class="c"># Class constructor...</span> | |
| 66 <a name="new-"></a> 53 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 67 54 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 68 55 | |
| 69 56 <span class="c"># Initialize object...</span> | |
| 70 57 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 71 58 <span class="k">bless</span> <span class="i">$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> | |
| 72 59 <span class="i">$This</span><span class="i">->_InitializeSDFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 73 60 | |
| 74 61 <span class="i">$This</span><span class="i">->_InitializeSDFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 75 62 | |
| 76 63 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 77 64 <span class="s">}</span> | |
| 78 65 | |
| 79 66 <span class="c"># Initialize any local object data...</span> | |
| 80 67 <span class="c">#</span> | |
| 81 <a name="_InitializeSDFileIO-"></a> 68 <span class="k">sub </span><span class="m">_InitializeSDFileIO</span> <span class="s">{</span> | |
| 82 69 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 83 70 | |
| 84 71 <span class="c"># Sorting of MDL data fields during output: Keep the initial order or write 'em out alphabetically...</span> | |
| 85 72 <span class="i">$This</span>->{<span class="w">SortDataFieldsDuringOutput</span>} = <span class="q">'No'</span><span class="sc">;</span> | |
| 86 73 | |
| 87 74 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 88 75 <span class="s">}</span> | |
| 89 76 | |
| 90 77 <span class="c"># Initialize class ...</span> | |
| 91 <a name="_InitializeClass-"></a> 78 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 92 79 <span class="c">#Class name...</span> | |
| 93 80 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 94 81 | |
| 95 82 <span class="s">}</span> | |
| 96 83 | |
| 97 84 <span class="c"># Initialize object values...</span> | |
| 98 <a name="_InitializeSDFileIOProperties-"></a> 85 <span class="k">sub </span><span class="m">_InitializeSDFileIOProperties</span> <span class="s">{</span> | |
| 99 86 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 100 87 | |
| 101 88 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> | |
| 102 89 <span class="c"># are implemented on-demand using ObjectProperty class.</span> | |
| 103 90 | |
| 104 91 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
| 105 92 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 106 93 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 107 94 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 108 95 <span class="s">}</span> | |
| 109 96 | |
| 110 97 <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> | |
| 111 98 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying file name..."</span><span class="sc">;</span> | |
| 112 99 <span class="s">}</span> | |
| 113 100 | |
| 114 101 <span class="c"># Make sure it's a SD file...</span> | |
| 115 102 <span class="i">$Name</span> = <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="sc">;</span> | |
| 116 103 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsSDFile</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 117 104 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $Name, doesn't appear to be SDF format..."</span><span class="sc">;</span> | |
| 118 105 <span class="s">}</span> | |
| 119 106 | |
| 120 107 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 121 108 <span class="s">}</span> | |
| 122 109 | |
| 123 110 <span class="c"># Is it a SD file?</span> | |
| 124 <a name="IsSDFile-"></a> 111 <span class="k">sub </span><span class="m">IsSDFile ($;$)</span> <span class="s">{</span> | |
| 125 112 <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> | |
| 126 113 <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">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 127 114 | |
| 128 115 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsSDFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 129 116 <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> | |
| 130 117 <span class="s">}</span> | |
| 131 118 <span class="k">else</span> <span class="s">{</span> | |
| 132 119 <span class="i">$FileName</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> | |
| 133 120 <span class="s">}</span> | |
| 134 121 | |
| 135 122 <span class="c"># Check file extension...</span> | |
| 136 123 <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">"sd sdf"</span><span class="s">)</span><span class="sc">;</span> | |
| 137 124 | |
| 138 125 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 139 126 <span class="s">}</span> | |
| 140 127 | |
| 141 128 <span class="c"># Read molecule from file and return molecule object...</span> | |
| 142 <a name="ReadMolecule-"></a> 129 <span class="k">sub </span><span class="m">ReadMolecule</span> <span class="s">{</span> | |
| 143 130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 144 131 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> | |
| 145 132 | |
| 146 133 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 147 134 <span class="k">return</span> <span class="i">$This</span><span class="i">->ParseMoleculeString</span><span class="s">(</span><span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 148 135 <span class="s">}</span> | |
| 149 136 | |
| 150 137 <span class="c"># Write compound data along with any data field label and values using Molecule object...</span> | |
| 151 <a name="WriteMolecule-"></a> 138 <span class="k">sub </span><span class="m">WriteMolecule</span> <span class="s">{</span> | |
| 152 139 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 153 140 | |
| 154 141 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$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> | |
| 155 142 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->WriteMolecule: No data written: Molecule object is not specified..."</span><span class="sc">;</span> | |
| 156 143 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 157 144 <span class="s">}</span> | |
| 158 145 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> | |
| 159 146 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 160 147 | |
| 161 148 <span class="k">print</span> <span class="i">$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> | |
| 162 149 | |
| 163 150 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 164 151 <span class="s">}</span> | |
| 165 152 | |
| 166 153 <span class="c"># Retrieve molecule string...</span> | |
| 167 <a name="ReadMoleculeString-"></a> 154 <span class="k">sub </span><span class="m">ReadMoleculeString</span> <span class="s">{</span> | |
| 168 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 169 156 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> | |
| 170 157 | |
| 171 158 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 172 159 <span class="k">return</span> <span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span> | |
| 173 160 <span class="s">}</span> | |
| 174 161 | |
| 175 162 <span class="c"># Parse molecule string and return molecule object. ParseMoleculeString supports two invocation methods: class</span> | |
| 176 163 <span class="c"># method or a package function.</span> | |
| 177 164 <span class="c">#</span> | |
| 178 <a name="ParseMoleculeString-"></a> 165 <span class="k">sub </span><span class="m">ParseMoleculeString</span> <span class="s">{</span> | |
| 179 166 <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> | |
| 180 167 <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> | |
| 181 168 | |
| 182 169 <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">_IsSDFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 183 170 <span class="s">(</span><span class="i">$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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 184 171 <span class="s">}</span> | |
| 185 172 <span class="k">else</span> <span class="s">{</span> | |
| 186 173 <span class="i">$MoleculeString</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> | |
| 187 174 <span class="i">$This</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 188 175 <span class="s">}</span> | |
| 189 176 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MoleculeString</span><span class="s">)</span> <span class="s">{</span> | |
| 190 177 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 191 178 <span class="s">}</span> | |
| 192 179 <span class="c"># Parse molecule data...</span> | |
| 193 180 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 194 181 <span class="i">$Molecule</span> = <span class="i">FileIO::MDLMolFileIO::ParseMoleculeString</span><span class="s">(</span><span class="i">$MoleculeString</span><span class="s">)</span><span class="sc">;</span> | |
| 195 182 | |
| 196 183 <span class="c"># Process data label/value pairs...</span> | |
| 197 184 <span class="k">my</span><span class="s">(</span><span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">@DataLabels</span><span class="cm">,</span> <span class="i">%DataLabelsAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 198 185 | |
| 199 186 <span class="i">%DataLabelsAndValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 200 187 <span class="i">@MoleculeLines</span> = <span class="k">split</span> <span class="q">/\n/</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="sc">;</span> | |
| 201 188 <span class="i">@DataLabels</span> = <span class="i">SDFileUtil::GetCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">@MoleculeLines</span><span class="s">)</span><span class="sc">;</span> | |
| 202 189 <span class="i">%DataLabelsAndValues</span> = <span class="i">SDFileUtil::GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@MoleculeLines</span><span class="s">)</span><span class="sc">;</span> | |
| 203 190 | |
| 204 191 <span class="c"># Store reference to data labels to keep track of their initial order in SD file...</span> | |
| 205 192 <span class="i">$Molecule</span><span class="i">->SetDataFieldLabels</span><span class="s">(</span>\<span class="i">@DataLabels</span><span class="s">)</span><span class="sc">;</span> | |
| 206 193 | |
| 207 194 <span class="c"># Store reference to SD data label/value pairs hash as a generic property of molecule...</span> | |
| 208 195 <span class="i">$Molecule</span><span class="i">->SetDataFieldLabelAndValues</span><span class="s">(</span>\<span class="i">%DataLabelsAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 209 196 | |
| 210 197 <span class="k">return</span> <span class="i">$Molecule</span><span class="sc">;</span> | |
| 211 198 <span class="s">}</span> | |
| 212 199 | |
| 213 200 <span class="c"># Generate molecule string using molecule object...</span> | |
| 214 <a name="GenerateMoleculeString-"></a> 201 <span class="k">sub </span><span class="m">GenerateMoleculeString</span> <span class="s">{</span> | |
| 215 202 <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> | |
| 216 203 <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> | |
| 217 204 | |
| 218 205 <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">_IsSDFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 219 206 <span class="s">(</span><span class="i">$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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 220 207 <span class="s">}</span> | |
| 221 208 <span class="k">else</span> <span class="s">{</span> | |
| 222 209 <span class="i">$Molecule</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> | |
| 223 210 <span class="i">$This</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 224 211 <span class="s">}</span> | |
| 225 212 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 226 213 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 227 214 <span class="s">}</span> | |
| 228 215 <span class="c"># Generate CTAB data...</span> | |
| 229 216 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span> | |
| 230 217 <span class="i">$CmpdString</span> = <span class="i">FileIO::MDLMolFileIO::GenerateMoleculeString</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 231 218 | |
| 232 219 <span class="c"># Generate any data field labels and values...</span> | |
| 233 220 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelsAndValuesString</span><span class="s">)</span><span class="sc">;</span> | |
| 234 221 | |
| 235 222 <span class="i">$DataFieldLabelsAndValuesString</span> = <span class="q">''</span><span class="sc">;</span> | |
| 236 223 <span class="k">if</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'DataFieldLabels'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 237 224 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelsRef</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="cm">,</span> <span class="i">$SortDataFields</span><span class="s">)</span><span class="sc">;</span> | |
| 238 225 | |
| 239 226 <span class="i">$SortDataFields</span> = <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">SortDataFieldsDuringOutput</span>}<span class="s">)</span> && <span class="i">$This</span>->{<span class="w">SortDataFieldsDuringOutput</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 240 227 | |
| 241 228 <span class="i">$DataFieldLabelsRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabels</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 242 229 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 243 230 <span class="i">$DataFieldLabelsAndValuesString</span> = <span class="k">join</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdDataHeaderLabelsAndValuesLines</span><span class="s">(</span><span class="i">$DataFieldLabelsRef</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="cm">,</span> <span class="i">$SortDataFields</span><span class="s">)</span><span class="sc">;</span> | |
| 244 231 <span class="s">}</span> | |
| 245 232 | |
| 246 233 <span class="k">return</span> <span class="q">"${CmpdString }\n${DataFieldLabelsAndValuesString}\n\$\$\$\$"</span><span class="sc">;</span> | |
| 247 234 <span class="s">}</span> | |
| 248 235 | |
| 249 236 | |
| 250 237 <span class="c"># Is it a SDFileIO object?</span> | |
| 251 <a name="_IsSDFileIO-"></a> 238 <span class="k">sub </span><span class="m">_IsSDFileIO</span> <span class="s">{</span> | |
| 252 239 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 253 240 | |
| 254 241 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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> | |
| 255 242 <span class="s">}</span> | |
| 256 243 | |
| 257 <a name="EOF-"></a></pre> | |
| 258 <p> </p> | |
| 259 <br /> | |
| 260 <center> | |
| 261 <img src="../../../images/h2o2.png"> | |
| 262 </center> | |
| 263 </body> | |
| 264 </html> |