Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/modules/html/code/MoleculeFileIO.html @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/MoleculeFileIO.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,246 @@ +<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>