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3 <title>MayaChemTools:Documentation:MoleculeFileIO.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./Molecule.html" title="Molecule.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/MoleculeFileIO.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/MoleculeFileIO.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/MoleculeFileIO.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/MoleculeFileIO.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
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20 <h2>NAME</h2>
21 <p>MoleculeFileIO</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use MoleculeFileIO;</p>
26 <p>use MoleculeFileIO qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>MoleculeFileIO</strong> class provides the following methods:</p>
31 <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>
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>IsSupportedMoleculeFileFormat</p>
35 <p>
36 </p>
37 <h2>METHODS</h2>
38 <dl>
39 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
40 <dd>
41 <div class="OptionsBox">
42 $NewMoleculeFileIO = new MoleculeFileIO([%PropertyNameAndValues]);</div>
43 <p>Using specified <em>MoleculeFileIO</em> property names and values hash, <strong>new</strong> method
44 creates a new object and returns a reference to newly created <strong>MoleculeFileIO</strong> object.
45 By default, following properties are initialized:</p>
46 <div class="OptionsBox">
47 Name = &quot;&quot;
48 <br/> Mode = &quot;&quot;
49 <br/> FileIORef = &quot;&quot;</div>
50 <p>Based on extension of specified file <em>Name</em>, an input class is automatically associated to
51 provide molecule read and write methods.</p>
52 <p>Examples:</p>
53 <div class="OptionsBox">
54 $Name = &quot;Water.mol&quot;;
55 <br/> $Mode = &quot;Read&quot;;
56 <br/> $MoleculeFileIO = new MoleculeFileIO('Name' =&gt; $Name,
57 'Mode' =&gt; $Mode);
58 <br/> $MoleculeFileIO-&gt;Open();
59 <br/> $Molecule = $MoleculeFileIO-&gt;ReadMolecule();
60 <br/> $Molecule-&gt;DetectRings();
61 <br/> print &quot;$Molecule\n&quot;;
62 <br/> $MoleculeFileIO-&gt;Close();</div>
63 <div class="OptionsBox">
64 $MoleculeFileIO = new MoleculeFileIO('Name' =&gt; 'Sample1.sdf',
65 'Mode' =&gt; 'Read');
66 <br/> $MoleculeFileIO-&gt;Open();
67 <br/> while ($Molecule = $MoleculeFileIO1-&gt;ReadMolecule()) {
68 <br/>&nbsp;&nbsp;&nbsp;&nbsp; $Molecule-&gt;DetectRings();
69 <br/>&nbsp;&nbsp;&nbsp;&nbsp; print &quot;$Molecule\n&quot;;</div>
70 <div class="OptionsBox">
71 &nbsp;&nbsp;&nbsp;&nbsp; $DataLabelsAndValuesRef =
72 $Molecule-&gt;GetDataFieldLabelAndValues();
73 <br/>&nbsp;&nbsp;&nbsp;&nbsp; for $DataLabel (sort keys %{$DataLabelsAndValuesRef} ) {
74 <br/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $DataValue = $DataLabelsAndValuesRef-&gt;{$DataLabel};
75 <br/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; print &quot;&lt;DataLabel: $DataLabel; DataValue: $DataValue&gt;; &quot;;
76 <br/>&nbsp;&nbsp;&nbsp;&nbsp; }
77 <br/>&nbsp;&nbsp;&nbsp;&nbsp; print &quot;\n&quot;;
78 <br/> }
79 <br/> $MoleculeFileIO-&gt;Close();</div>
80 </dd>
81 <dt><strong><a name="close" class="item"><strong>Close</strong></a></strong></dt>
82 <dd>
83 <div class="OptionsBox">
84 $MoleculeFileIO-&gt;Close();</div>
85 <p>Closes an open file</p>
86 </dd>
87 <dt><strong><a name="issupportedmoleculefileformat" class="item"><strong>IsSupportedMoleculeFileFormat</strong></a></strong></dt>
88 <dd>
89 <div class="OptionsBox">
90 $Status = $MoleculeFileIO-&gt;IsSupportedMoleculeFileFormat($Name);
91 <br/> $Status = MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
92 <br/> ($Status, $FormatType, $IOClassName) =
93 $MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);</div>
94 <p>Returns 1 or 0 based on whether input file <em>Name</em> format is supported. In list context,
95 value of supported format type and name of associated IO class is also returned.</p>
96 <p>File extension is used to determine file format. Currently, following file extensions are
97 supported:</p>
98 <div class="OptionsBox">
99 FileExts - FormatType - AssociatedIOClassName</div>
100 <div class="OptionsBox">
101 .mol - MDLMOL - MDLMolFileIO
102 <br/> .sdf, .sd - SDF - SDFileIO</div>
103 </dd>
104 <dt><strong><a name="open" class="item"><strong>Open</strong></a></strong></dt>
105 <dd>
106 <div class="OptionsBox">
107 $MoleculeFileIO-&gt;Open([$Mode]);</div>
108 <p>Opens a file in a specified <em>Mode</em>. Default mode value: <em>Read</em>. Supported mode
109 values:</p>
110 <div class="OptionsBox">
111 Read, Write, Append, &lt;, &gt;, &gt;&gt;, r, w, or a</div>
112 </dd>
113 <dt><strong><a name="readmolecule" class="item"><strong>ReadMolecule</strong></a></strong></dt>
114 <dd>
115 <div class="OptionsBox">
116 $Molecule = $MoleculeFileIO-&gt;ReadMolecule();</div>
117 <p>Reads molecule data from the file and returns a <em>Molecule</em> object.</p>
118 </dd>
119 <dt><strong><a name="readmoleculestring" class="item"><strong>ReadMoleculeString</strong></a></strong></dt>
120 <dd>
121 <div class="OptionsBox">
122 $MoleculeString = $MoleculeFileIO-&gt;ReadMoleculeString();</div>
123 <p>Reads molecule data from a file and returns a <em>Molecule</em> string.</p>
124 </dd>
125 <dt><strong><a name="writemolecule" class="item"><strong>WriteMolecule</strong></a></strong></dt>
126 <dd>
127 <div class="OptionsBox">
128 $MoleculeFileIO-&gt;WriteMolecule();</div>
129 <p>Write molecule data to a file for a <em>Molecule</em>.</p>
130 </dd>
131 </dl>
132 <p>
133 </p>
134 <h2>AUTHOR</h2>
135 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
136 <p>
137 </p>
138 <h2>SEE ALSO</h2>
139 <p><a href="./FileIO.html">FileIO.pm</a>,&nbsp<a href="./MDLMolFileIO.html">MDLMolFileIO.pm</a>,&nbsp<a href="./SDFileIO.html">SDFileIO.pm</a>
140 </p>
141 <p>
142 </p>
143 <h2>COPYRIGHT</h2>
144 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
145 <p>This file is part of MayaChemTools.</p>
146 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
147 the terms of the GNU Lesser General Public License as published by the Free
148 Software Foundation; either version 3 of the License, or (at your option)
149 any later version.</p>
150 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
151 <table width="100%" border=0 cellpadding=0 cellspacing=2>
152 <tr align="left" valign="top"><td width="33%" align="left"><a href="./Molecule.html" title="Molecule.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>
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