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| author | deepakjadmin |
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| date | Thu, 15 Dec 2016 14:18:03 -0500 |
| parents | 73ae111cf86f |
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<html> <head> <title>MayaChemTools:Documentation:MoleculeFileIO.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.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/> <div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <p> </p> <h2>NAME</h2> <p>MoleculeFileIO</p> <p> </p> <h2>SYNOPSIS</h2> <p>use MoleculeFileIO;</p> <p>use MoleculeFileIO qw(:all);</p> <p> </p> <h2>DESCRIPTION</h2> <p><strong>MoleculeFileIO</strong> class provides the following methods:</p> <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> , <a href="#readmoleculestring">ReadMoleculeString</a>, <a href="#writemolecule">WriteMolecule</a> </p><p>The following methods can also be used as functions:</p> <p>IsSupportedMoleculeFileFormat</p> <p> </p> <h2>METHODS</h2> <dl> <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> <dd> <div class="OptionsBox"> $NewMoleculeFileIO = new MoleculeFileIO([%PropertyNameAndValues]);</div> <p>Using specified <em>MoleculeFileIO</em> property names and values hash, <strong>new</strong> method creates a new object and returns a reference to newly created <strong>MoleculeFileIO</strong> object. By default, following properties are initialized:</p> <div class="OptionsBox"> Name = "" <br/> Mode = "" <br/> FileIORef = ""</div> <p>Based on extension of specified file <em>Name</em>, an input class is automatically associated to provide molecule read and write methods.</p> <p>Examples:</p> <div class="OptionsBox"> $Name = "Water.mol"; <br/> $Mode = "Read"; <br/> $MoleculeFileIO = new MoleculeFileIO('Name' => $Name, 'Mode' => $Mode); <br/> $MoleculeFileIO->Open(); <br/> $Molecule = $MoleculeFileIO->ReadMolecule(); <br/> $Molecule->DetectRings(); <br/> print "$Molecule\n"; <br/> $MoleculeFileIO->Close();</div> <div class="OptionsBox"> $MoleculeFileIO = new MoleculeFileIO('Name' => 'Sample1.sdf', 'Mode' => 'Read'); <br/> $MoleculeFileIO->Open(); <br/> while ($Molecule = $MoleculeFileIO1->ReadMolecule()) { <br/> $Molecule->DetectRings(); <br/> print "$Molecule\n";</div> <div class="OptionsBox"> $DataLabelsAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); <br/> for $DataLabel (sort keys %{$DataLabelsAndValuesRef} ) { <br/> $DataValue = $DataLabelsAndValuesRef->{$DataLabel}; <br/> print "<DataLabel: $DataLabel; DataValue: $DataValue>; "; <br/> } <br/> print "\n"; <br/> } <br/> $MoleculeFileIO->Close();</div> </dd> <dt><strong><a name="close" class="item"><strong>Close</strong></a></strong></dt> <dd> <div class="OptionsBox"> $MoleculeFileIO->Close();</div> <p>Closes an open file</p> </dd> <dt><strong><a name="issupportedmoleculefileformat" class="item"><strong>IsSupportedMoleculeFileFormat</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Status = $MoleculeFileIO->IsSupportedMoleculeFileFormat($Name); <br/> $Status = MoleculeFileIO::IsSupportedMoleculeFileFormat($Name); <br/> ($Status, $FormatType, $IOClassName) = $MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);</div> <p>Returns 1 or 0 based on whether input file <em>Name</em> format is supported. In list context, value of supported format type and name of associated IO class is also returned.</p> <p>File extension is used to determine file format. Currently, following file extensions are supported:</p> <div class="OptionsBox"> FileExts - FormatType - AssociatedIOClassName</div> <div class="OptionsBox"> .mol - MDLMOL - MDLMolFileIO <br/> .sdf, .sd - SDF - SDFileIO</div> </dd> <dt><strong><a name="open" class="item"><strong>Open</strong></a></strong></dt> <dd> <div class="OptionsBox"> $MoleculeFileIO->Open([$Mode]);</div> <p>Opens a file in a specified <em>Mode</em>. Default mode value: <em>Read</em>. Supported mode values:</p> <div class="OptionsBox"> Read, Write, Append, <, >, >>, r, w, or a</div> </dd> <dt><strong><a name="readmolecule" class="item"><strong>ReadMolecule</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Molecule = $MoleculeFileIO->ReadMolecule();</div> <p>Reads molecule data from the file and returns a <em>Molecule</em> object.</p> </dd> <dt><strong><a name="readmoleculestring" class="item"><strong>ReadMoleculeString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $MoleculeString = $MoleculeFileIO->ReadMoleculeString();</div> <p>Reads molecule data from a file and returns a <em>Molecule</em> string.</p> </dd> <dt><strong><a name="writemolecule" class="item"><strong>WriteMolecule</strong></a></strong></dt> <dd> <div class="OptionsBox"> $MoleculeFileIO->WriteMolecule();</div> <p>Write molecule data to a file for a <em>Molecule</em>.</p> </dd> </dl> <p> </p> <h2>AUTHOR</h2> <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> <p> </p> <h2>SEE ALSO</h2> <p><a href="./FileIO.html">FileIO.pm</a>, <a href="./MDLMolFileIO.html">MDLMolFileIO.pm</a>, <a href="./SDFileIO.html">SDFileIO.pm</a> </p> <p> </p> <h2>COPYRIGHT</h2> <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> <p>This file is part of MayaChemTools.</p> <p>MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.</p> <p> </p><p> </p><div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>