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1 <html>
2 <head>
3 <title>MayaChemTools:Documentation:FileIO::MDLMolFileIO.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FingerprintsTextFileIO.html" title="FingerprintsTextFileIO.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./SDFileIO.html" title="SDFileIO.html">Next</a></td><td width="34%" align="middle"><strong>FileIO::MDLMolFileIO.pm</strong></td><td width="33%" align="right"><a href="././code/MDLMolFileIO.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/MDLMolFileIO.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/MDLMolFileIO.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/MDLMolFileIO.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/MDLMolFileIO.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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17 </div>
18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>MDLMolFileIO</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use FileIO::MDLMolFileIO;</p>
26 <p>use FileIO::MDLMolFileIO qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>MDLMolFIleIO</strong> class provides the following methods:</p>
31 <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>
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>GenerateMoleculeString, IsMDLMolFile, ParseMoleculeString</p>
35 <p>Data specific to <strong>MDLMolFileIO</strong> class not directly used by <strong>Molecule</strong>, <strong>Atom</strong> and
36 <strong>Bond</strong> objects - data label/value pairs, atom SteroParity and so on - is associated to
37 and retrieved from appropriate objects using following methods:</p>
38 <div class="OptionsBox">
39 SetMDL&lt;PropertyName&gt;
40 <br/> GetMDL&lt;PropertyName&gt;.</div>
41 <p><strong>MDLMolFileIO</strong> class is derived from <em>FileIO</em> class and uses its methods to support
42 generic file related functionality.</p>
43 <p>
44 </p>
45 <h2>METHODS</h2>
46 <dl>
47 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
48 <dd>
49 <div class="OptionsBox">
50 $NewMDLMolFileIO = new FileIO::MDLMolFileIO(%NamesAndValues);</div>
51 <p>Using specified <em>MDLMolFileIO</em> property names and values hash, <strong>new</strong> method creates a new object
52 and returns a reference to newly created <strong>MDLMolFileIO</strong> object.</p>
53 </dd>
54 <dt><strong><a name="generatemoleculestring" class="item"><strong>GenerateMoleculeString</strong></a></strong></dt>
55 <dd>
56 <div class="OptionsBox">
57 $MoleculeString = $MDLMolFileIO-&gt;GenerateMoleculeString($Molecule);
58 <br/> $MoleculeString = FileIO::MDLMolFileIO::GenerateMoleculeString($Molecule);</div>
59 <p>Returns a <strong>MoleculeString</strong> in MDLMol format corresponding to <em>Molecule</em>.</p>
60 </dd>
61 <dt><strong><a name="ismdlmolfile" class="item"><strong>IsMDLMolFile</strong></a></strong></dt>
62 <dd>
63 <div class="OptionsBox">
64 $Status = $MDLMolFileIO-&gt;IsMDLMolFile($FileName);
65 <br/> $Status = FileIO::MDLMolFileIO::IsMDLMolFile($FileName);</div>
66 <p>Returns 1 or 0 based on whether <em>FileName</em> is a MDLMol file.</p>
67 </dd>
68 <dt><strong><a name="parsemoleculestring" class="item"><strong>ParseMoleculeString</strong></a></strong></dt>
69 <dd>
70 <div class="OptionsBox">
71 $Molecule = $MDLMolFileIO-&gt;ParseMoleculeString($MoleculeString);
72 <br/> $Molecule = FileIO::MDLMolFileIO::ParseMoleculeString($MoleculeString);</div>
73 <p>Parses <em>MoleculeString</em> and returns a <strong>Molecule</strong> object.</p>
74 </dd>
75 <dt><strong><a name="readmolecule" class="item"><strong>ReadMolecule</strong></a></strong></dt>
76 <dd>
77 <div class="OptionsBox">
78 $Molecule = $MDLMolFileIO-&gt;ReadMolecule($FileHandle);</div>
79 <p>Reads data for the compound in a file using already opened <em>FileHandle</em>, creates,
80 and returns a <strong>Molecule</strong> object.</p>
81 </dd>
82 <dt><strong><a name="readmoleculestring" class="item"><strong>ReadMoleculeString</strong></a></strong></dt>
83 <dd>
84 <div class="OptionsBox">
85 $MoleculeString = $MDLMolFileIO-&gt;ReadMoleculeString($FileHandle);</div>
86 <p>Reads data for the compound in a file using already opened <em>FileHandle</em> and
87 returns a <strong>MoleculeString</strong> corresponding to compound structure and other associated
88 data.</p>
89 </dd>
90 <dt><strong><a name="writemolecule" class="item"><strong>WriteMolecule</strong></a></strong></dt>
91 <dd>
92 <div class="OptionsBox">
93 $MDLMolFileIO-&gt;WriteMolecule($Molecule);</div>
94 <p>Writes <em>Molecule</em> data to a file in MDLMol format and returns <strong>MDLMolFileIO</strong>.</p>
95 </dd>
96 </dl>
97 <p>
98 </p>
99 <h2>AUTHOR</h2>
100 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
101 <p>
102 </p>
103 <h2>SEE ALSO</h2>
104 <p><a href="./MoleculeFileIO.html">MoleculeFileIO.pm</a>,&nbsp<a href="./SDFileIO.html">SDFileIO.pm</a>
105 </p>
106 <p>
107 </p>
108 <h2>COPYRIGHT</h2>
109 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
110 <p>This file is part of MayaChemTools.</p>
111 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
112 the terms of the GNU Lesser General Public License as published by the Free
113 Software Foundation; either version 3 of the License, or (at your option)
114 any later version.</p>
115 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
116 <table width="100%" border=0 cellpadding=0 cellspacing=2>
117 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FingerprintsTextFileIO.html" title="FingerprintsTextFileIO.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./SDFileIO.html" title="SDFileIO.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>FileIO::MDLMolFileIO.pm</strong></td></tr>
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