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