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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:MoleculeFileIO.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.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 <div class="DocNav"> | |
| 14 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./Molecule.html" title="Molecule.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./NucleicAcids.html" title="NucleicAcids.html">Next</a></td><td width="34%" align="middle"><strong>MoleculeFileIO.pm</strong></td><td width="33%" align="right"><a href="././code/MoleculeFileIO.html" title="View source code">Code</a> | <a href="./../pdf/MoleculeFileIO.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MoleculeFileIO.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MoleculeFileIO.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MoleculeFileIO.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> | |
| 16 </table> | |
| 17 </div> | |
| 18 <p> | |
| 19 </p> | |
| 20 <h2>NAME</h2> | |
| 21 <p>MoleculeFileIO</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>use MoleculeFileIO;</p> | |
| 26 <p>use MoleculeFileIO qw(:all);</p> | |
| 27 <p> | |
| 28 </p> | |
| 29 <h2>DESCRIPTION</h2> | |
| 30 <p><strong>MoleculeFileIO</strong> class provides the following methods:</p> | |
| 31 <p> <a href="#new">new</a>, <a href="#close">Close</a>, <a href="#issupportedmoleculefileformat">IsSupportedMoleculeFileFormat</a>, <a href="#open">Open</a>, <a href="#readmolecule">ReadMolecule</a> | |
| 32 , <a href="#readmoleculestring">ReadMoleculeString</a>, <a href="#writemolecule">WriteMolecule</a> | |
| 33 </p><p>The following methods can also be used as functions:</p> | |
| 34 <p>IsSupportedMoleculeFileFormat</p> | |
| 35 <p> | |
| 36 </p> | |
| 37 <h2>METHODS</h2> | |
| 38 <dl> | |
| 39 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> | |
| 40 <dd> | |
| 41 <div class="OptionsBox"> | |
| 42 $NewMoleculeFileIO = new MoleculeFileIO([%PropertyNameAndValues]);</div> | |
| 43 <p>Using specified <em>MoleculeFileIO</em> property names and values hash, <strong>new</strong> method | |
| 44 creates a new object and returns a reference to newly created <strong>MoleculeFileIO</strong> object. | |
| 45 By default, following properties are initialized:</p> | |
| 46 <div class="OptionsBox"> | |
| 47 Name = "" | |
| 48 <br/> Mode = "" | |
| 49 <br/> FileIORef = ""</div> | |
| 50 <p>Based on extension of specified file <em>Name</em>, an input class is automatically associated to | |
| 51 provide molecule read and write methods.</p> | |
| 52 <p>Examples:</p> | |
| 53 <div class="OptionsBox"> | |
| 54 $Name = "Water.mol"; | |
| 55 <br/> $Mode = "Read"; | |
| 56 <br/> $MoleculeFileIO = new MoleculeFileIO('Name' => $Name, | |
| 57 'Mode' => $Mode); | |
| 58 <br/> $MoleculeFileIO->Open(); | |
| 59 <br/> $Molecule = $MoleculeFileIO->ReadMolecule(); | |
| 60 <br/> $Molecule->DetectRings(); | |
| 61 <br/> print "$Molecule\n"; | |
| 62 <br/> $MoleculeFileIO->Close();</div> | |
| 63 <div class="OptionsBox"> | |
| 64 $MoleculeFileIO = new MoleculeFileIO('Name' => 'Sample1.sdf', | |
| 65 'Mode' => 'Read'); | |
| 66 <br/> $MoleculeFileIO->Open(); | |
| 67 <br/> while ($Molecule = $MoleculeFileIO1->ReadMolecule()) { | |
| 68 <br/> $Molecule->DetectRings(); | |
| 69 <br/> print "$Molecule\n";</div> | |
| 70 <div class="OptionsBox"> | |
| 71 $DataLabelsAndValuesRef = | |
| 72 $Molecule->GetDataFieldLabelAndValues(); | |
| 73 <br/> for $DataLabel (sort keys %{$DataLabelsAndValuesRef} ) { | |
| 74 <br/> $DataValue = $DataLabelsAndValuesRef->{$DataLabel}; | |
| 75 <br/> print "<DataLabel: $DataLabel; DataValue: $DataValue>; "; | |
| 76 <br/> } | |
| 77 <br/> print "\n"; | |
| 78 <br/> } | |
| 79 <br/> $MoleculeFileIO->Close();</div> | |
| 80 </dd> | |
| 81 <dt><strong><a name="close" class="item"><strong>Close</strong></a></strong></dt> | |
| 82 <dd> | |
| 83 <div class="OptionsBox"> | |
| 84 $MoleculeFileIO->Close();</div> | |
| 85 <p>Closes an open file</p> | |
| 86 </dd> | |
| 87 <dt><strong><a name="issupportedmoleculefileformat" class="item"><strong>IsSupportedMoleculeFileFormat</strong></a></strong></dt> | |
| 88 <dd> | |
| 89 <div class="OptionsBox"> | |
| 90 $Status = $MoleculeFileIO->IsSupportedMoleculeFileFormat($Name); | |
| 91 <br/> $Status = MoleculeFileIO::IsSupportedMoleculeFileFormat($Name); | |
| 92 <br/> ($Status, $FormatType, $IOClassName) = | |
| 93 $MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);</div> | |
| 94 <p>Returns 1 or 0 based on whether input file <em>Name</em> format is supported. In list context, | |
| 95 value of supported format type and name of associated IO class is also returned.</p> | |
| 96 <p>File extension is used to determine file format. Currently, following file extensions are | |
| 97 supported:</p> | |
| 98 <div class="OptionsBox"> | |
| 99 FileExts - FormatType - AssociatedIOClassName</div> | |
| 100 <div class="OptionsBox"> | |
| 101 .mol - MDLMOL - MDLMolFileIO | |
| 102 <br/> .sdf, .sd - SDF - SDFileIO</div> | |
| 103 </dd> | |
| 104 <dt><strong><a name="open" class="item"><strong>Open</strong></a></strong></dt> | |
| 105 <dd> | |
| 106 <div class="OptionsBox"> | |
| 107 $MoleculeFileIO->Open([$Mode]);</div> | |
| 108 <p>Opens a file in a specified <em>Mode</em>. Default mode value: <em>Read</em>. Supported mode | |
| 109 values:</p> | |
| 110 <div class="OptionsBox"> | |
| 111 Read, Write, Append, <, >, >>, r, w, or a</div> | |
| 112 </dd> | |
| 113 <dt><strong><a name="readmolecule" class="item"><strong>ReadMolecule</strong></a></strong></dt> | |
| 114 <dd> | |
| 115 <div class="OptionsBox"> | |
| 116 $Molecule = $MoleculeFileIO->ReadMolecule();</div> | |
| 117 <p>Reads molecule data from the file and returns a <em>Molecule</em> object.</p> | |
| 118 </dd> | |
| 119 <dt><strong><a name="readmoleculestring" class="item"><strong>ReadMoleculeString</strong></a></strong></dt> | |
| 120 <dd> | |
| 121 <div class="OptionsBox"> | |
| 122 $MoleculeString = $MoleculeFileIO->ReadMoleculeString();</div> | |
| 123 <p>Reads molecule data from a file and returns a <em>Molecule</em> string.</p> | |
| 124 </dd> | |
| 125 <dt><strong><a name="writemolecule" class="item"><strong>WriteMolecule</strong></a></strong></dt> | |
| 126 <dd> | |
| 127 <div class="OptionsBox"> | |
| 128 $MoleculeFileIO->WriteMolecule();</div> | |
| 129 <p>Write molecule data to a file for a <em>Molecule</em>.</p> | |
| 130 </dd> | |
| 131 </dl> | |
| 132 <p> | |
| 133 </p> | |
| 134 <h2>AUTHOR</h2> | |
| 135 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 136 <p> | |
| 137 </p> | |
| 138 <h2>SEE ALSO</h2> | |
| 139 <p><a href="./FileIO.html">FileIO.pm</a>, <a href="./MDLMolFileIO.html">MDLMolFileIO.pm</a>, <a href="./SDFileIO.html">SDFileIO.pm</a> | |
| 140 </p> | |
| 141 <p> | |
| 142 </p> | |
| 143 <h2>COPYRIGHT</h2> | |
| 144 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 145 <p>This file is part of MayaChemTools.</p> | |
| 146 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 147 the terms of the GNU Lesser General Public License as published by the Free | |
| 148 Software Foundation; either version 3 of the License, or (at your option) | |
| 149 any later version.</p> | |
| 150 <p> </p><p> </p><div class="DocNav"> | |
| 151 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 152 <tr align="left" valign="top"><td width="33%" align="left"><a href="./Molecule.html" title="Molecule.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./NucleicAcids.html" title="NucleicAcids.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MoleculeFileIO.pm</strong></td></tr> | |
| 153 </table> | |
| 154 </div> | |
| 155 <br /> | |
| 156 <center> | |
| 157 <img src="../../images/h2o2.png"> | |
| 158 </center> | |
| 159 </body> | |
| 160 </html> |