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3 <title>MayaChemTools:Documentation:FileIO::MDLMolFileIO.pm</title>
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11 </center>
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13 <div class="DocNav">
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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="./FingerprintsTextFileIO.html" title="FingerprintsTextFileIO.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/MDLMolFileIO.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MDLMolFileIO.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MDLMolFileIO.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MDLMolFileIO.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>MDLMolFileIO</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::MDLMolFileIO;</p>
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26 <p>use FileIO::MDLMolFileIO 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>MDLMolFIleIO</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="#ismdlmolfile">IsMDLMolFile</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, IsMDLMolFile, ParseMoleculeString</p>
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35 <p>Data specific to <strong>MDLMolFileIO</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 appropriate 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><strong>MDLMolFileIO</strong> class is derived from <em>FileIO</em> class and uses its methods to support
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42 generic file related functionality.</p>
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43 <p>
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44 </p>
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45 <h2>METHODS</h2>
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46 <dl>
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47 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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48 <dd>
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49 <div class="OptionsBox">
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50 $NewMDLMolFileIO = new FileIO::MDLMolFileIO(%NamesAndValues);</div>
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51 <p>Using specified <em>MDLMolFileIO</em> property names and values hash, <strong>new</strong> method creates a new object
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52 and returns a reference to newly created <strong>MDLMolFileIO</strong> object.</p>
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53 </dd>
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54 <dt><strong><a name="generatemoleculestring" class="item"><strong>GenerateMoleculeString</strong></a></strong></dt>
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55 <dd>
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56 <div class="OptionsBox">
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57 $MoleculeString = $MDLMolFileIO->GenerateMoleculeString($Molecule);
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58 <br/> $MoleculeString = FileIO::MDLMolFileIO::GenerateMoleculeString($Molecule);</div>
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59 <p>Returns a <strong>MoleculeString</strong> in MDLMol format corresponding to <em>Molecule</em>.</p>
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60 </dd>
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61 <dt><strong><a name="ismdlmolfile" class="item"><strong>IsMDLMolFile</strong></a></strong></dt>
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62 <dd>
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63 <div class="OptionsBox">
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64 $Status = $MDLMolFileIO->IsMDLMolFile($FileName);
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65 <br/> $Status = FileIO::MDLMolFileIO::IsMDLMolFile($FileName);</div>
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66 <p>Returns 1 or 0 based on whether <em>FileName</em> is a MDLMol file.</p>
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67 </dd>
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68 <dt><strong><a name="parsemoleculestring" class="item"><strong>ParseMoleculeString</strong></a></strong></dt>
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69 <dd>
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70 <div class="OptionsBox">
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71 $Molecule = $MDLMolFileIO->ParseMoleculeString($MoleculeString);
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72 <br/> $Molecule = FileIO::MDLMolFileIO::ParseMoleculeString($MoleculeString);</div>
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73 <p>Parses <em>MoleculeString</em> and returns a <strong>Molecule</strong> object.</p>
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74 </dd>
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75 <dt><strong><a name="readmolecule" class="item"><strong>ReadMolecule</strong></a></strong></dt>
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76 <dd>
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77 <div class="OptionsBox">
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78 $Molecule = $MDLMolFileIO->ReadMolecule($FileHandle);</div>
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79 <p>Reads data for the compound in a file using already opened <em>FileHandle</em>, creates,
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80 and returns a <strong>Molecule</strong> object.</p>
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81 </dd>
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82 <dt><strong><a name="readmoleculestring" class="item"><strong>ReadMoleculeString</strong></a></strong></dt>
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83 <dd>
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84 <div class="OptionsBox">
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85 $MoleculeString = $MDLMolFileIO->ReadMoleculeString($FileHandle);</div>
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86 <p>Reads data for the compound in a file using already opened <em>FileHandle</em> and
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87 returns a <strong>MoleculeString</strong> corresponding to compound structure and other associated
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88 data.</p>
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89 </dd>
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90 <dt><strong><a name="writemolecule" class="item"><strong>WriteMolecule</strong></a></strong></dt>
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91 <dd>
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92 <div class="OptionsBox">
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93 $MDLMolFileIO->WriteMolecule($Molecule);</div>
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94 <p>Writes <em>Molecule</em> data to a file in MDLMol format and returns <strong>MDLMolFileIO</strong>.</p>
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95 </dd>
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96 </dl>
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97 <p>
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98 </p>
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99 <h2>AUTHOR</h2>
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100 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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101 <p>
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102 </p>
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103 <h2>SEE ALSO</h2>
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104 <p><a href="./MoleculeFileIO.html">MoleculeFileIO.pm</a>, <a href="./SDFileIO.html">SDFileIO.pm</a>
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105 </p>
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106 <p>
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107 </p>
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108 <h2>COPYRIGHT</h2>
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109 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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110 <p>This file is part of MayaChemTools.</p>
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111 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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112 the terms of the GNU Lesser General Public License as published by the Free
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113 Software Foundation; either version 3 of the License, or (at your option)
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114 any later version.</p>
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115 <p> </p><p> </p><div class="DocNav">
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116 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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117 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FingerprintsTextFileIO.html" title="FingerprintsTextFileIO.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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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118 </table>
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