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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/SDFileIO.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,137 @@ +<html> +<head> +<title>MayaChemTools:Documentation:FileIO::SDFileIO.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="./MDLMolFileIO.html" title="MDLMolFileIO.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FileUtil.html" title="FileUtil.html">Next</a></td><td width="34%" align="middle"><strong>FileIO::SDFileIO.pm</strong></td><td width="33%" align="right"><a href="././code/SDFileIO.html" title="View source code">Code</a> | <a href="./../pdf/SDFileIO.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/SDFileIO.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/SDFileIO.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/SDFileIO.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>SDFileIO</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use FileIO::SDFileIO;</p> +<p>use FileIO::SDFileIO qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>SDFIleIO</strong> class provides the following methods:</p> +<p> <a href="#new">new</a>, <a href="#generatemoleculestring">GenerateMoleculeString</a>, <a href="#issdfile">IsSDFile</a>, <a href="#parsemoleculestring">ParseMoleculeString</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>GenerateMoleculeString, IsSDFile, ParseMoleculeString</p> +<p>Data specific to <strong>SDFileIO</strong> class not directly used by <strong>Molecule</strong>, <strong>Atom</strong> and +<strong>Bond</strong> objects - data label/value pairs, atom SteroParity and so on - is associated to +and retrieved from approptiate objects using following methods:</p> +<div class="OptionsBox"> + SetMDL<PropertyName> +<br/> GetMDL<PropertyName>.</div> +<p>SD data label and values are attached to <strong>Molecule</strong> object as a refernece to a hash +using SetDataFieldLabelAndValues and can be retrieved using GetDataFieldLabelAndValues +method.</p> +<p><strong>SDFileIO</strong> class is derived from <em>FileIO</em> class and uses its methods to support +generic file related functionality.</p> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewSDFileIO = new FileIO::SDFileIO(%NamesAndValues);</div> +<p>Using specified <em>SDFileIO</em> property names and values hash, <strong>new</strong> method creates a new object +and returns a reference to newly created <strong>SDFileIO</strong> object.</p> +</dd> +<dt><strong><a name="generatemoleculestring" class="item"><strong>GenerateMoleculeString</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MoleculeString = $SDFileIO->GenerateMoleculeString($Molecule); +<br/> $MoleculeString = FileIO::SDFileIO::GenerateMoleculeString($Molecule);</div> +<p>Returns a <strong>MoleculeString</strong> in SD format corresponding to <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="issdfile" class="item"><strong>IsSDFile</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $SDFileIO->IsSDFile($FileName); +<br/> $Status = FileIO::SDFileIO::IsSDFile($FileName);</div> +<p>Returns 1 or 0 based on whether <em>FileName</em> is a SD file.</p> +</dd> +<dt><strong><a name="parsemoleculestring" class="item"><strong>ParseMoleculeString</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule = $SDFileIO->ParseMoleculeString($MoleculeString); +<br/> $Molecule = FileIO::SDFileIO::ParseMoleculeString($MoleculeString);</div> +<p>Parses <em>MoleculeString</em> and returns a <strong>Molecule</strong> object. SD data field label and value pairs +are associated to <strong>Molecule</strong> object as a reference to a hash using:</p> +<div class="OptionsBox"> + $Molecule->SetDataFieldLabelAndValues(\%DataLabelsAndValues)</div> +<p>The reference to hash can be retrieved by:</p> +<div class="OptionsBox"> + $DataLabelsAndValues = $Molecule->GetDataFieldLabelAndValues(); +<br/> for $DataLabel (sort keys %{$DataLabelsAndValues}) { +<br/> $DataValue = $DataLabelsAndValues->{$DataLabel}; +<br/> }</div> +</dd> +<dt><strong><a name="readmolecule" class="item"><strong>ReadMolecule</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule = $SDFileIO->ReadMolecule($FileHandle);</div> +<p>Reads data for the next compound in a file using already opened <em>FileHandle</em>, creates, +and returns a <strong>Molecule</strong> object.</p> +</dd> +<dt><strong><a name="readmoleculestring" class="item"><strong>ReadMoleculeString</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MoleculeString = $SDFileIO->ReadMoleculeString($FileHandle);</div> +<p>Reads data for the next compound in a file using already opened <em>FileHandle</em> and +returns a <strong>MoleculeString</strong> corresponding to compound structure and other associated +data.</p> +</dd> +<dt><strong><a name="writemolecule" class="item"><strong>WriteMolecule</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $SDFileIO->WriteMolecule($Molecule);</div> +<p>Writes <em>Molecule</em> data to a file in MDLMol format and returns <strong>SDFileIO</strong>.</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="./MoleculeFileIO.html">MoleculeFileIO.pm</a>, <a href="./MDLMolFileIO.html">MDLMolFileIO.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="./MDLMolFileIO.html" title="MDLMolFileIO.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FileUtil.html" title="FileUtil.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>FileIO::SDFileIO.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>