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3 <title>MayaChemTools:Documentation:SplitSDFiles.pl</title>
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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="./SortTextFiles.html" title="SortTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SplitTextFiles.html" title="SplitTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>SplitSDFiles.pl</strong></td><td width="33%" align="right"><a href="././code/SplitSDFiles.html" title="View source code">Code</a> | <a href="./../pdf/SplitSDFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/SplitSDFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/SplitSDFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/SplitSDFiles.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>SplitSDFiles.pl - Split SDFile(s) into multiple SD files</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>SplitSDFiles.pl SDFile(s)...</p>
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26 <p>SplitSDFiles.pl [<strong>-c, --CmpdsMode</strong> DataField | MolName | RootPrefix]
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27 [<strong>-d, --DataField</strong> DataFieldName] [<strong>-h, --help</strong>] [<strong>-m, --mode</strong> Cmpds | Files]
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28 [<strong>-n, --numfiles</strong> number] [<strong>--numcmpds</strong> number] [<strong>-o, --overwrite</strong>]
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29 [<strong>-r, --root</strong> rootname] [<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>Split <em>SDFile(s)</em> into multiple SD files. Each new SDFile contains a compound
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34 subset of similar size from the initial file. Multiple <em>SDFile(s)</em> names are separated
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35 by space. The valid file extensions are <em>.sdf</em> and <em>.sd</em>. All other file names are
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36 ignored. All the SD files in a current directory can be specified either by <em>*.sdf</em>
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37 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>-c, --CmpdsMode</strong> <em>DataField | MolName | RootPrefix</em></strong></dt>
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43 <dd>
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44 <p>This option is only used during <em>Cmpds</em> value of <-m, --mode> option with
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45 specified <strong>--numcmpds</strong> value of 1.</p>
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46 <p>Specify how to generate new file names during <em>Cmpds</em> value of <-m, --mode>
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47 option: use <em>SDFile(s)</em> datafield value or molname line for a specific compound;
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48 generate a sequential ID using root prefix specified by <strong>-r, --root</strong> option.</p>
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49 <p>Possible values: <em>DataField | MolName | RootPrefix | RootPrefix</em>.
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50 Default: <em>RootPrefix</em>.</p>
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51 <p>For empty <em>MolName</em> and <em>DataField</em> values during these specified modes, file
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52 name is automatically generated using <em>RootPrefix</em>.</p>
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53 <p>For <em>RootPrefix</em> value of <strong>-c, --CmpdsMode</strong> option, new file names are
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54 generated using by appending compound record number to value of <strong>-r, --root</strong> option.
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55 For example: <em>RootName</em>Cmd<RecordNumber>.sdf.</p>
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56 <p>Allowed characters in file names are: a-zA-Z0-9_. All other characters in datafield
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57 values, molname line, and root prefix are ignore during generation of file names.</p>
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58 </dd>
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59 <dt><strong><strong>-d, --DataField</strong> <em>DataFieldName</em></strong></dt>
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60 <dd>
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61 <p>This option is only used during <em>DataField</em> value of <-c, --CmpdsMode> option.</p>
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62 <p>Specify <em>SDFile(s)</em> datafield label name whose value is used for generation of new file
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63 for a specific compound. Default value: <em>None</em>.</p>
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64 </dd>
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65 <dt><strong><strong>-h, --help</strong></strong></dt>
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66 <dd>
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67 <p>Print this help message.</p>
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68 </dd>
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69 <dt><strong><strong>-m, --mode</strong> <em>Cmpds | Files</em></strong></dt>
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70 <dd>
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71 <p>Specify how to split <em>SDFile(s)</em>: split into files with each file containing specified
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72 number of compounds or split into a specified number of files.</p>
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73 <p>Possible values: <em>Cmpds | Files</em>. Default: <em>Files</em>.</p>
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74 <p>For <em>Cmpds</em> value of <strong>-m, --mode</strong> option, value of <strong>--numcmpds</strong> option
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75 determines the number of new files. And value of <strong>-n, --numfiles</strong> option is
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76 used to figure out the number of new files for <em>Files</em> value of <strong>-m, --mode</strong> option.</p>
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77 </dd>
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78 <dt><strong><strong>-n, --numfiles</strong> <em>number</em></strong></dt>
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79 <dd>
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80 <p>Number of new files to generate for each <em>SDFile(s)</em>. Default: <em>2</em>.</p>
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81 <p>This value is only used during <em>Files</em> value of <strong>-m, --mode</strong> option.</p>
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82 </dd>
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83 <dt><strong><strong>--numcmpds</strong> <em>number</em></strong></dt>
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84 <dd>
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85 <p>Number of compounds in each new file corresponding to each <em>SDFile(s)</em>.
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86 Default: <em>1</em>.</p>
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87 <p>This value is only used during <em>Cmpds</em> value of <strong>-m, --mode</strong> option.</p>
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88 </dd>
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89 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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90 <dd>
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91 <p>Overwrite existing files.</p>
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92 </dd>
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93 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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94 <dd>
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95 <p>New SD file names are generated using the root: <Root>Part<Count>.sdf.
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96 Default new file names: <InitialSDFileName> Part<Count>.sdf. This option
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97 is ignored for multiple input files.</p>
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98 </dd>
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99 <dt><strong><strong>-w,--workingdir</strong> <em>dirname</em></strong></dt>
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100 <dd>
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101 <p>Location of working directory. Default: current directory.</p>
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102 </dd>
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103 </dl>
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104 <p>
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105 </p>
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106 <h2>EXAMPLES</h2>
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107 <p>To split each SD file into 5 new SD files, type:</p>
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108 <div class="ExampleBox">
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109 % SplitSDFiles.pl -n 5 -o Sample1.sdf Sample2.sdf
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110 <br/>% SplitSDFiles.pl -n 5 -o *.sdf</div>
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111 <p>To split Sample1.sdf into 10 new NewSample*.sdf files, type:</p>
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112 <div class="ExampleBox">
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113 % SplitSDFiles.pl -m Files -n 10 -r NewSample -o Sample1.sdf</div>
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114 <p>To split Sample1.sdf into new NewSample*.sdf files containing maximum of 5 compounds
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115 in each file, type:</p>
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116 <div class="ExampleBox">
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117 % SplitSDFiles.pl -m Cmpds --numcmpds 5 -r NewSample -o Sample1.sdf</div>
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118 <p>To split Sample1.sdf into new SD files containing one compound each with new file
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119 names corresponding to molname line, type:</p>
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120 <div class="ExampleBox">
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121 % SplitSDFiles.pl -m Cmpds --numcmpds 1 -c MolName -o Sample1.sdf</div>
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122 <p>To split Sample1.sdf into new SD files containing one compound each with new file
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123 names corresponding to value of datafield MolID, type:</p>
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124 <div class="ExampleBox">
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125 % SplitSDFiles.pl -m Cmpds --numcmpds 1 -c DataField -d MolID
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126 -o Sample1.sdf</div>
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127 <p>
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128 </p>
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129 <h2>AUTHOR</h2>
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130 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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131 <p>
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132 </p>
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133 <h2>SEE ALSO</h2>
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134 <p><a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./JoinSDFiles.html">JoinSDFiles.pl</a>, <a href="./MolFilesToSD.html">MolFilesToSD.pl</a>, <a href="./SDToMolFiles.html">SDToMolFiles.pl</a>
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135 </p>
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136 <p>
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137 </p>
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138 <h2>COPYRIGHT</h2>
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139 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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140 <p>This file is part of MayaChemTools.</p>
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141 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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142 the terms of the GNU Lesser General Public License as published by the Free
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143 Software Foundation; either version 3 of the License, or (at your option)
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144 any later version.</p>
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145 <p> </p><p> </p><div class="DocNav">
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146 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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147 <tr align="left" valign="top"><td width="33%" align="left"><a href="./SortTextFiles.html" title="SortTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SplitTextFiles.html" title="SplitTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>SplitSDFiles.pl</strong></td></tr>
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148 </table>
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149 </div>
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150 <br />
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151 <center>
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152 <img src="../../images/h2o2.png">
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