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<title>MayaChemTools:Documentation:FileIO::MDLMolFileIO.pm</title>
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<h2>NAME</h2>
<p>MDLMolFileIO</p>
<p>
</p>
<h2>SYNOPSIS</h2>
<p>use FileIO::MDLMolFileIO;</p>
<p>use FileIO::MDLMolFileIO qw(:all);</p>
<p>
</p>
<h2>DESCRIPTION</h2>
<p><strong>MDLMolFIleIO</strong> class provides the following methods:</p>
<p> <a href="#new">new</a>, <a href="#generatemoleculestring">GenerateMoleculeString</a>, <a href="#ismdlmolfile">IsMDLMolFile</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, IsMDLMolFile, ParseMoleculeString</p>
<p>Data specific to <strong>MDLMolFileIO</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 appropriate objects using following methods:</p>
<div class="OptionsBox">
    SetMDL&lt;PropertyName&gt;
<br/>    GetMDL&lt;PropertyName&gt;.</div>
<p><strong>MDLMolFileIO</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">
    $NewMDLMolFileIO = new FileIO::MDLMolFileIO(%NamesAndValues);</div>
<p>Using specified <em>MDLMolFileIO</em> property names and values hash, <strong>new</strong> method creates a new object
and returns a reference to newly created <strong>MDLMolFileIO</strong> object.</p>
</dd>
<dt><strong><a name="generatemoleculestring" class="item"><strong>GenerateMoleculeString</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $MoleculeString = $MDLMolFileIO-&gt;GenerateMoleculeString($Molecule);
<br/>    $MoleculeString = FileIO::MDLMolFileIO::GenerateMoleculeString($Molecule);</div>
<p>Returns a <strong>MoleculeString</strong> in MDLMol format corresponding to <em>Molecule</em>.</p>
</dd>
<dt><strong><a name="ismdlmolfile" class="item"><strong>IsMDLMolFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $Status = $MDLMolFileIO-&gt;IsMDLMolFile($FileName);
<br/>    $Status = FileIO::MDLMolFileIO::IsMDLMolFile($FileName);</div>
<p>Returns 1 or 0 based on whether <em>FileName</em> is a MDLMol file.</p>
</dd>
<dt><strong><a name="parsemoleculestring" class="item"><strong>ParseMoleculeString</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $Molecule = $MDLMolFileIO-&gt;ParseMoleculeString($MoleculeString);
<br/>    $Molecule = FileIO::MDLMolFileIO::ParseMoleculeString($MoleculeString);</div>
<p>Parses <em>MoleculeString</em> and returns a <strong>Molecule</strong> object.</p>
</dd>
<dt><strong><a name="readmolecule" class="item"><strong>ReadMolecule</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $Molecule = $MDLMolFileIO-&gt;ReadMolecule($FileHandle);</div>
<p>Reads data for the 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 = $MDLMolFileIO-&gt;ReadMoleculeString($FileHandle);</div>
<p>Reads data for the 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">
    $MDLMolFileIO-&gt;WriteMolecule($Molecule);</div>
<p>Writes <em>Molecule</em> data to a file in MDLMol format and returns <strong>MDLMolFileIO</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>,&nbsp<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>
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