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3 <title>MayaChemTools:Documentation:SDToMolFiles.pl</title>
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10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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11 </center>
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12 <br/>
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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="./SDFilesToHTML.html" title="SDFilesToHTML.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SimilarityMatricesFingerprints.html" title="SimilarityMatricesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>SDToMolFiles.pl</strong></td><td width="33%" align="right"><a href="././code/SDToMolFiles.html" title="View source code">Code</a> | <a href="./../pdf/SDToMolFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/SDToMolFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/SDToMolFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/SDToMolFiles.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>SDToMolFiles.pl - Generate MDLMOL file(s) from SD file(s)</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>SDToMolFiles.pl SDFile(s)...</p>
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26 <p>SDToMolFiles.pl [<strong>-d, --DataField</strong> DataFieldName]
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27 [<strong>-m, --mode</strong> DataField | MolName | RootPrefix] [<strong>-h, --help</strong>]
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28 [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname]
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29 [<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p>
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30 <p>
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31 </p>
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32 <h2>DESCRIPTION</h2>
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33 <p>Generate MDLMOL file(s) from <em>SDFile(s)</em>. All header data labels and values in
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34 SDFile(s) are simply ignored; other appopriate data from SDFile(s) is transferred to MDLMOL
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35 files. Multiple <em>SDFile(s)</em> names are separated by spaces. The valid file extensions are
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36 <em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a current
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37 directory can be specified either by <em>*.sdf</em> or the current directory name.</p>
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38 <p>
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39 </p>
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40 <h2>OPTIONS</h2>
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41 <dl>
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42 <dt><strong><strong>-d, --DataField</strong> <em>DataFieldName</em></strong></dt>
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43 <dd>
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44 <p>Specify <em>SDFile(s)</em> datafield label name whose value is used for generation of MDLMOL
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45 file names. Default value: <em>None</em>.</p>
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46 </dd>
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47 <dt><strong><strong>-h, --help</strong></strong></dt>
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48 <dd>
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49 <p>Print this help message.</p>
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50 </dd>
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51 <dt><strong><strong>-m, --mode</strong> <em>DataField | MolName | RootPrefix</em></strong></dt>
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52 <dd>
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53 <p>Specify how to generate MDLMOL file names: use a <em>SDFile(s)</em> datafield value; use
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54 molname line from <em>SDFile(s)</em>; generate a sequential ID using root prefix specified
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55 by <strong>-r, --root</strong> option.</p>
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56 <p>Possible values: <em>DataField | MolName | RootPrefix | RootPrefix</em>.
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57 Default: <em>RootPrefix</em>.</p>
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58 <p>For empty <em>MolName</em> and <em>DataField</em> values during these specified modes, file
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59 name is automatically generated using <em>RootPrefix</em>.</p>
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60 <p>For <em>RootPrefix</em> value of <strong>-m, --mode</strong> option, MDLMOL file names are generated
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61 using by appending compound record number to value of <strong>-r, --root</strong> option. For
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62 example: <em>RootName</em>Cmd<RecordNumber>.mol.</p>
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63 <p>Allowed characters in file names are: a-zA-Z0-9_. All other characters in datafield
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64 values, molname line, and root prefix are ignore during generation of file names.</p>
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65 </dd>
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66 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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67 <dd>
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68 <p>Overwrite existing files.</p>
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69 </dd>
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70 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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71 <dd>
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72 <p>Specify root name to used during <em>RootPrefix</em> <strong>-m, --mode</strong> option value.
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73 New MDLMOL file names are generated using the root: <Root>Cmpd<RecordNumber>.mol
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74 Default for new file names: <InitialSDFileName>Cmpd<RecordNumber>.mol. This option
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75 is ignored for multiple input files.</p>
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76 </dd>
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77 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
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78 <dd>
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79 <p>Location of working directory. Default: current directory.</p>
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80 </dd>
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81 </dl>
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82 <p>
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83 </p>
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84 <h2>EXAMPLES</h2>
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85 <p>To generate MDLMOL files from Sample1*.sdf and Sample2*.sd files, type:</p>
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86 <div class="ExampleBox">
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87 % SDToMolFiles.pl -o Sample1*.sdf Sample2*.sd</div>
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88 <p>To generate Sample*.mol files from Sample1.sdf, type:</p>
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89 <div class="ExampleBox">
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90 % SDToMolFiles.pl -r Sample -o Sample1.sdf</div>
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91 <p>To generate MOL files from Sample1.sdf using molname line data for generating
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92 MOL file names, type:</p>
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93 <div class="ExampleBox">
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94 % SDToMolFiles.pl -m MolName -r Sample -o Sample1.sdf</div>
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95 <p>To generate MOL files from Sample1.sdf using a specific data field values for
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96 generating MOL file names, type:</p>
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97 <div class="ExampleBox">
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98 % SDToMolFiles.pl -m DataField --DataField MolID -r Sample
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99 -o Sample1.sdf</div>
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100 <p>
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101 </p>
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102 <h2>AUTHOR</h2>
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103 <p>
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104 </p>
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105 <h2>AUTHOR</h2>
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106 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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107 <p>
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108 </p>
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109 <h2>SEE ALSO</h2>
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110 <p><a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./MolFilesToSD.html">MolFilesToSD.pl</a>
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111 </p>
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112 <p>
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113 </p>
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114 <h2>COPYRIGHT</h2>
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115 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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116 <p>This file is part of MayaChemTools.</p>
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117 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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118 the terms of the GNU Lesser General Public License as published by the Free
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119 Software Foundation; either version 3 of the License, or (at your option)
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120 any later version.</p>
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121 <p> </p><p> </p><div class="DocNav">
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122 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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123 <tr align="left" valign="top"><td width="33%" align="left"><a href="./SDFilesToHTML.html" title="SDFilesToHTML.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SimilarityMatricesFingerprints.html" title="SimilarityMatricesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>SDToMolFiles.pl</strong></td></tr>
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124 </table>
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125 </div>
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126 <br />
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127 <center>
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128 <img src="../../images/h2o2.png">
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