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3 <title>MayaChemTools:Documentation:MoleculeFileIO.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="./Molecule.html" title="Molecule.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/MoleculeFileIO.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MoleculeFileIO.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MoleculeFileIO.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MoleculeFileIO.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>MoleculeFileIO</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 MoleculeFileIO;</p>
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26 <p>use MoleculeFileIO 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>MoleculeFileIO</strong> class provides the following methods:</p>
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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>
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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>IsSupportedMoleculeFileFormat</p>
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35 <p>
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36 </p>
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37 <h2>METHODS</h2>
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38 <dl>
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39 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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40 <dd>
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41 <div class="OptionsBox">
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42 $NewMoleculeFileIO = new MoleculeFileIO([%PropertyNameAndValues]);</div>
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43 <p>Using specified <em>MoleculeFileIO</em> property names and values hash, <strong>new</strong> method
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44 creates a new object and returns a reference to newly created <strong>MoleculeFileIO</strong> object.
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45 By default, following properties are initialized:</p>
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46 <div class="OptionsBox">
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47 Name = ""
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48 <br/> Mode = ""
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49 <br/> FileIORef = ""</div>
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50 <p>Based on extension of specified file <em>Name</em>, an input class is automatically associated to
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51 provide molecule read and write methods.</p>
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52 <p>Examples:</p>
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53 <div class="OptionsBox">
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54 $Name = "Water.mol";
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55 <br/> $Mode = "Read";
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56 <br/> $MoleculeFileIO = new MoleculeFileIO('Name' => $Name,
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57 'Mode' => $Mode);
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58 <br/> $MoleculeFileIO->Open();
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59 <br/> $Molecule = $MoleculeFileIO->ReadMolecule();
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60 <br/> $Molecule->DetectRings();
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61 <br/> print "$Molecule\n";
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62 <br/> $MoleculeFileIO->Close();</div>
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63 <div class="OptionsBox">
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64 $MoleculeFileIO = new MoleculeFileIO('Name' => 'Sample1.sdf',
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65 'Mode' => 'Read');
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66 <br/> $MoleculeFileIO->Open();
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67 <br/> while ($Molecule = $MoleculeFileIO1->ReadMolecule()) {
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68 <br/> $Molecule->DetectRings();
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69 <br/> print "$Molecule\n";</div>
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70 <div class="OptionsBox">
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71 $DataLabelsAndValuesRef =
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72 $Molecule->GetDataFieldLabelAndValues();
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73 <br/> for $DataLabel (sort keys %{$DataLabelsAndValuesRef} ) {
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74 <br/> $DataValue = $DataLabelsAndValuesRef->{$DataLabel};
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75 <br/> print "<DataLabel: $DataLabel; DataValue: $DataValue>; ";
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76 <br/> }
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77 <br/> print "\n";
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78 <br/> }
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79 <br/> $MoleculeFileIO->Close();</div>
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80 </dd>
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81 <dt><strong><a name="close" class="item"><strong>Close</strong></a></strong></dt>
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82 <dd>
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83 <div class="OptionsBox">
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84 $MoleculeFileIO->Close();</div>
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85 <p>Closes an open file</p>
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86 </dd>
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87 <dt><strong><a name="issupportedmoleculefileformat" class="item"><strong>IsSupportedMoleculeFileFormat</strong></a></strong></dt>
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88 <dd>
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89 <div class="OptionsBox">
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90 $Status = $MoleculeFileIO->IsSupportedMoleculeFileFormat($Name);
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91 <br/> $Status = MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
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92 <br/> ($Status, $FormatType, $IOClassName) =
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93 $MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);</div>
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94 <p>Returns 1 or 0 based on whether input file <em>Name</em> format is supported. In list context,
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95 value of supported format type and name of associated IO class is also returned.</p>
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96 <p>File extension is used to determine file format. Currently, following file extensions are
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97 supported:</p>
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98 <div class="OptionsBox">
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99 FileExts - FormatType - AssociatedIOClassName</div>
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100 <div class="OptionsBox">
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101 .mol - MDLMOL - MDLMolFileIO
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102 <br/> .sdf, .sd - SDF - SDFileIO</div>
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103 </dd>
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104 <dt><strong><a name="open" class="item"><strong>Open</strong></a></strong></dt>
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105 <dd>
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106 <div class="OptionsBox">
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107 $MoleculeFileIO->Open([$Mode]);</div>
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108 <p>Opens a file in a specified <em>Mode</em>. Default mode value: <em>Read</em>. Supported mode
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109 values:</p>
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110 <div class="OptionsBox">
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111 Read, Write, Append, <, >, >>, r, w, or a</div>
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112 </dd>
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113 <dt><strong><a name="readmolecule" class="item"><strong>ReadMolecule</strong></a></strong></dt>
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114 <dd>
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115 <div class="OptionsBox">
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116 $Molecule = $MoleculeFileIO->ReadMolecule();</div>
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117 <p>Reads molecule data from the file and returns a <em>Molecule</em> object.</p>
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118 </dd>
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119 <dt><strong><a name="readmoleculestring" class="item"><strong>ReadMoleculeString</strong></a></strong></dt>
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120 <dd>
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121 <div class="OptionsBox">
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122 $MoleculeString = $MoleculeFileIO->ReadMoleculeString();</div>
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123 <p>Reads molecule data from a file and returns a <em>Molecule</em> string.</p>
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124 </dd>
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125 <dt><strong><a name="writemolecule" class="item"><strong>WriteMolecule</strong></a></strong></dt>
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126 <dd>
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127 <div class="OptionsBox">
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128 $MoleculeFileIO->WriteMolecule();</div>
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129 <p>Write molecule data to a file for a <em>Molecule</em>.</p>
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130 </dd>
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131 </dl>
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132 <p>
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133 </p>
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134 <h2>AUTHOR</h2>
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135 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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136 <p>
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137 </p>
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138 <h2>SEE ALSO</h2>
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139 <p><a href="./FileIO.html">FileIO.pm</a>, <a href="./MDLMolFileIO.html">MDLMolFileIO.pm</a>, <a href="./SDFileIO.html">SDFileIO.pm</a>
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140 </p>
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141 <p>
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142 </p>
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143 <h2>COPYRIGHT</h2>
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144 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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145 <p>This file is part of MayaChemTools.</p>
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146 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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147 the terms of the GNU Lesser General Public License as published by the Free
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148 Software Foundation; either version 3 of the License, or (at your option)
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149 any later version.</p>
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150 <p> </p><p> </p><div class="DocNav">
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151 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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152 <tr align="left" valign="top"><td width="33%" align="left"><a href="./Molecule.html" title="Molecule.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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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153 </table>
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154 </div>
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155 <br />
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156 <center>
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157 <img src="../../images/h2o2.png">
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