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3 <title>MayaChemTools:Documentation:FileIO::SDFileIO.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MDLMolFileIO.html" title="MDLMolFileIO.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/SDFileIO.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/SDFileIO.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/SDFileIO.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/SDFileIO.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>SDFileIO</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use FileIO::SDFileIO;</p>
26 <p>use FileIO::SDFileIO qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>SDFIleIO</strong> class provides the following methods:</p>
31 <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>
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, IsSDFile, ParseMoleculeString</p>
35 <p>Data specific to <strong>SDFileIO</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 approptiate objects using following methods:</p>
38 <div class="OptionsBox">
39 SetMDL&lt;PropertyName&gt;
40 <br/> GetMDL&lt;PropertyName&gt;.</div>
41 <p>SD data label and values are attached to <strong>Molecule</strong> object as a refernece to a hash
42 using SetDataFieldLabelAndValues and can be retrieved using GetDataFieldLabelAndValues
43 method.</p>
44 <p><strong>SDFileIO</strong> class is derived from <em>FileIO</em> class and uses its methods to support
45 generic file related functionality.</p>
46 <p>
47 </p>
48 <h2>METHODS</h2>
49 <dl>
50 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
51 <dd>
52 <div class="OptionsBox">
53 $NewSDFileIO = new FileIO::SDFileIO(%NamesAndValues);</div>
54 <p>Using specified <em>SDFileIO</em> property names and values hash, <strong>new</strong> method creates a new object
55 and returns a reference to newly created <strong>SDFileIO</strong> object.</p>
56 </dd>
57 <dt><strong><a name="generatemoleculestring" class="item"><strong>GenerateMoleculeString</strong></a></strong></dt>
58 <dd>
59 <div class="OptionsBox">
60 $MoleculeString = $SDFileIO-&gt;GenerateMoleculeString($Molecule);
61 <br/> $MoleculeString = FileIO::SDFileIO::GenerateMoleculeString($Molecule);</div>
62 <p>Returns a <strong>MoleculeString</strong> in SD format corresponding to <em>Molecule</em>.</p>
63 </dd>
64 <dt><strong><a name="issdfile" class="item"><strong>IsSDFile</strong></a></strong></dt>
65 <dd>
66 <div class="OptionsBox">
67 $Status = $SDFileIO-&gt;IsSDFile($FileName);
68 <br/> $Status = FileIO::SDFileIO::IsSDFile($FileName);</div>
69 <p>Returns 1 or 0 based on whether <em>FileName</em> is a SD file.</p>
70 </dd>
71 <dt><strong><a name="parsemoleculestring" class="item"><strong>ParseMoleculeString</strong></a></strong></dt>
72 <dd>
73 <div class="OptionsBox">
74 $Molecule = $SDFileIO-&gt;ParseMoleculeString($MoleculeString);
75 <br/> $Molecule = FileIO::SDFileIO::ParseMoleculeString($MoleculeString);</div>
76 <p>Parses <em>MoleculeString</em> and returns a <strong>Molecule</strong> object. SD data field label and value pairs
77 are associated to <strong>Molecule</strong> object as a reference to a hash using:</p>
78 <div class="OptionsBox">
79 $Molecule-&gt;SetDataFieldLabelAndValues(\%DataLabelsAndValues)</div>
80 <p>The reference to hash can be retrieved by:</p>
81 <div class="OptionsBox">
82 $DataLabelsAndValues = $Molecule-&gt;GetDataFieldLabelAndValues();
83 <br/> for $DataLabel (sort keys %{$DataLabelsAndValues}) {
84 <br/>&nbsp;&nbsp;&nbsp;&nbsp; $DataValue = $DataLabelsAndValues-&gt;{$DataLabel};
85 <br/> }</div>
86 </dd>
87 <dt><strong><a name="readmolecule" class="item"><strong>ReadMolecule</strong></a></strong></dt>
88 <dd>
89 <div class="OptionsBox">
90 $Molecule = $SDFileIO-&gt;ReadMolecule($FileHandle);</div>
91 <p>Reads data for the next compound in a file using already opened <em>FileHandle</em>, creates,
92 and returns a <strong>Molecule</strong> object.</p>
93 </dd>
94 <dt><strong><a name="readmoleculestring" class="item"><strong>ReadMoleculeString</strong></a></strong></dt>
95 <dd>
96 <div class="OptionsBox">
97 $MoleculeString = $SDFileIO-&gt;ReadMoleculeString($FileHandle);</div>
98 <p>Reads data for the next compound in a file using already opened <em>FileHandle</em> and
99 returns a <strong>MoleculeString</strong> corresponding to compound structure and other associated
100 data.</p>
101 </dd>
102 <dt><strong><a name="writemolecule" class="item"><strong>WriteMolecule</strong></a></strong></dt>
103 <dd>
104 <div class="OptionsBox">
105 $SDFileIO-&gt;WriteMolecule($Molecule);</div>
106 <p>Writes <em>Molecule</em> data to a file in MDLMol format and returns <strong>SDFileIO</strong>.</p>
107 </dd>
108 </dl>
109 <p>
110 </p>
111 <h2>AUTHOR</h2>
112 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
113 <p>
114 </p>
115 <h2>SEE ALSO</h2>
116 <p><a href="./MoleculeFileIO.html">MoleculeFileIO.pm</a>,&nbsp<a href="./MDLMolFileIO.html">MDLMolFileIO.pm</a>
117 </p>
118 <p>
119 </p>
120 <h2>COPYRIGHT</h2>
121 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
122 <p>This file is part of MayaChemTools.</p>
123 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
124 the terms of the GNU Lesser General Public License as published by the Free
125 Software Foundation; either version 3 of the License, or (at your option)
126 any later version.</p>
127 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
128 <table width="100%" border=0 cellpadding=0 cellspacing=2>
129 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MDLMolFileIO.html" title="MDLMolFileIO.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>
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