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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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<html> <head> <title>MayaChemTools:Code:MoleculeFileIO.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> <a name="package-MoleculeFileIO-"></a> 1 <span class="k">package </span><span class="i">MoleculeFileIO</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: MoleculeFileIO.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span> 5 <span class="c"># $Revision: 1.32 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">FileIO::SDFileIO</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">FileIO::MDLMolFileIO</span><span class="sc">;</span> 35 36 <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> 37 38 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span> 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw(IsSupportedMoleculeFileFormat)</span><span class="sc">;</span> 41 42 <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> 43 44 <span class="c"># Setup class variables...</span> 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 47 48 <span class="c"># Class constructor...</span> <a name="new-"></a> 49 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 50 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 51 52 <span class="c"># Initialize object...</span> 53 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> 54 <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">$Class</span><span class="sc">;</span> 55 <span class="i">$This</span><span class="i">->_InitializeMoleculeFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 56 57 <span class="i">$This</span><span class="i">->_InitializeMoleculeFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 58 59 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 60 <span class="s">}</span> 61 62 <span class="c"># Initialize object data...</span> 63 <span class="c">#</span> <a name="_InitializeMoleculeFileIO-"></a> 64 <span class="k">sub </span><span class="m">_InitializeMoleculeFileIO</span> <span class="s">{</span> 65 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 66 67 <span class="c"># Reference to specific FileIO object...</span> 68 <span class="i">$This</span>->{<span class="w">FileIORef</span>} = <span class="q">''</span><span class="sc">;</span> 69 70 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 71 <span class="s">}</span> 72 73 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 74 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 75 <span class="c">#Class name...</span> 76 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 77 78 <span class="s">}</span> 79 80 <span class="c"># Initialize object properties......</span> 81 <span class="c">#</span> <a name="_InitializeMoleculeFileIOProperties-"></a> 82 <span class="k">sub </span><span class="m">_InitializeMoleculeFileIOProperties</span> <span class="s">{</span> 83 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 84 85 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="s">)</span> <span class="s">{</span> 86 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying file name..."</span><span class="sc">;</span> 87 <span class="s">}</span> 88 89 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Mode</span>}<span class="s">)</span> <span class="s">{</span> 90 <span class="i">$NamesAndValues</span>{<span class="w">Mode</span>} = <span class="q">'Read'</span><span class="sc">;</span> 91 <span class="s">}</span> 92 93 <span class="c"># Make sure its a supported format and intialize FileIO object reference...</span> 94 <span class="i">$This</span><span class="i">->_SetFileIORef</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 95 96 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 97 <span class="s">}</span> 98 99 <span class="c"># Setup FileIO object reference...</span> <a name="_SetFileIORef-"></a> 100 <span class="k">sub </span><span class="m">_SetFileIORef</span> <span class="s">{</span> 101 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 102 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$Format</span><span class="cm">,</span> <span class="i">$IOPackageName</span><span class="s">)</span><span class="sc">;</span> 103 104 <span class="i">$Name</span> = <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="sc">;</span> 105 106 <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$Format</span><span class="cm">,</span> <span class="i">$IOPackageName</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->IsSupportedMoleculeFileFormat</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="sc">;</span> 107 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span> 108 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File format, $Name, is not supported: Currently supported file formats are: SDF, MDLMol..."</span><span class="sc">;</span> 109 <span class="s">}</span> 110 111 <span class="i">$This</span>->{<span class="w">FileIORef</span>} = <span class="i">$</span>{<span class="w">IOPackageName</span>}<span class="i">->new</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 112 113 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 114 <span class="s">}</span> 115 116 <span class="c"># Is it a supported file format?</span> 117 <span class="c">#</span> 118 <span class="c"># In scalar context only status is returned; otherwise, file format and file IO package name is also</span> 119 <span class="c"># returned.</span> 120 <span class="c">#</span> 121 <span class="c"># Note:</span> 122 <span class="c"># . To support additional file formats, this is the only method which needs to be changed.</span> 123 <span class="c">#</span> 124 <span class="c"># . Currently supported file formats are:</span> 125 <span class="c">#</span> 126 <span class="c"># SDF .sdf, .sd</span> 127 <span class="c"># MDLMol .mol</span> 128 <span class="c">#</span> <a name="IsSupportedMoleculeFileFormat-"></a> 129 <span class="k">sub </span><span class="m">IsSupportedMoleculeFileFormat</span> <span class="s">{</span> 130 <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> 131 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Name</span><span class="s">)</span><span class="sc">;</span> 132 133 <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">_IsMoleculeFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 134 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Name</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> 135 <span class="s">}</span> 136 <span class="k">else</span> <span class="s">{</span> 137 <span class="s">(</span><span class="i">$Name</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> 138 <span class="s">}</span> 139 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$Format</span><span class="cm">,</span> <span class="i">$IOPackageName</span><span class="s">)</span><span class="sc">;</span> 140 141 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Format</span> = <span class="q">'NotSupported'</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">'Unknown'</span><span class="sc">;</span> 142 143 <span class="j">FORMAT:</span> <span class="s">{</span> 144 <span class="k">if</span> <span class="s">(</span><span class="i">FileIO::SDFileIO::IsSDFile</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$Format</span> = <span class="q">'SDF'</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">'FileIO::SDFileIO'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span> 145 <span class="k">if</span> <span class="s">(</span><span class="i">FileIO::MDLMolFileIO::IsMDLMolFile</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$Format</span> = <span class="q">'MDLMol'</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">'FileIO::MDLMolFileIO'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span> 146 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Format</span> = <span class="q">'NotSupported'</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">'Unknown'</span><span class="sc">;</span> 147 <span class="s">}</span> 148 149 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$Format</span><span class="cm">,</span> <span class="i">$IOPackageName</span><span class="s">)</span> <span class="co">:</span> <span class="i">$Status</span><span class="sc">;</span> 150 <span class="s">}</span> 151 152 <span class="c"># Prohibit file ref change...</span> 153 <span class="c">#</span> <a name="SetFileIORef-"></a> 154 <span class="k">sub </span><span class="m">SetFileIORef</span> <span class="s">{</span> 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 156 157 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFileIORef: Explicit setting of file ref is not supported..."</span><span class="sc">;</span> 158 159 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 160 <span class="s">}</span> 161 162 <span class="c"># Prohibit file name change...</span> 163 <span class="c">#</span> <a name="SetName-"></a> 164 <span class="k">sub </span><span class="m">SetName</span> <span class="s">{</span> 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Name</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 166 167 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetName: Explicit setting of file name is not supported: It must be set during object instantiation..."</span><span class="sc">;</span> 168 169 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 170 <span class="s">}</span> 171 172 <span class="c"># Prohibit file mode change...</span> 173 <span class="c">#</span> <a name="SetMode-"></a> 174 <span class="k">sub </span><span class="m">SetMode</span> <span class="s">{</span> 175 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 176 177 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMode: Explicit setting of file mode is not supported: It must be set during object instantiation..."</span><span class="sc">;</span> 178 179 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 180 <span class="s">}</span> 181 182 <span class="c"># Open file in a specific mode; default mode is Read only.</span> 183 <span class="c"># Supported mode values are: Read, Write, Append, <, >, >>, r, w, a</span> 184 <span class="c">#</span> <a name="Open-"></a> 185 <span class="k">sub </span><span class="m">Open</span> <span class="s">{</span> 186 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 187 188 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FileIORef</span>}<span class="i">->Open</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="sc">;</span> 189 <span class="s">}</span> 190 191 <span class="c"># close file...</span> <a name="Close-"></a> 192 <span class="k">sub </span><span class="m">Close</span> <span class="s">{</span> 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 194 195 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FileIORef</span>}<span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 196 <span class="s">}</span> 197 198 <span class="c"># Read molecule string from file and return a molecule object...</span> <a name="ReadMolecule-"></a> 199 <span class="k">sub </span><span class="m">ReadMolecule</span> <span class="s">{</span> 200 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 201 202 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FileIORef</span>}<span class="i">->ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 203 <span class="s">}</span> 204 205 <span class="c"># Retrieve molecule string from file...</span> <a name="ReadMoleculeString-"></a> 206 <span class="k">sub </span><span class="m">ReadMoleculeString</span> <span class="s">{</span> 207 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 208 209 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FileIORef</span>}<span class="i">->ReadMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 210 <span class="s">}</span> 211 212 <span class="c"># Write molecule using molecule object...</span> <a name="WriteMolecule-"></a> 213 <span class="k">sub </span><span class="m">WriteMolecule</span> <span class="s">{</span> 214 <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> 215 216 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FileIORef</span>}<span class="i">->WriteMolecule</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 217 <span class="s">}</span> 218 219 <span class="c"># Is it a MoleculeFileIO object?</span> <a name="_IsMoleculeFileIO-"></a> 220 <span class="k">sub </span><span class="m">_IsMoleculeFileIO</span> <span class="s">{</span> 221 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 222 223 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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> 224 <span class="s">}</span> 225 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>