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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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| -1:000000000000 | 0:4816e4a8ae95 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:SplitSDFiles.pl</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <div class="DocNav"> | |
| 14 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 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> | |
| 16 </table> | |
| 17 </div> | |
| 18 <p> | |
| 19 </p> | |
| 20 <h2>NAME</h2> | |
| 21 <p>SplitSDFiles.pl - Split SDFile(s) into multiple SD files</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>SplitSDFiles.pl SDFile(s)...</p> | |
| 26 <p>SplitSDFiles.pl [<strong>-c, --CmpdsMode</strong> DataField | MolName | RootPrefix] | |
| 27 [<strong>-d, --DataField</strong> DataFieldName] [<strong>-h, --help</strong>] [<strong>-m, --mode</strong> Cmpds | Files] | |
| 28 [<strong>-n, --numfiles</strong> number] [<strong>--numcmpds</strong> number] [<strong>-o, --overwrite</strong>] | |
| 29 [<strong>-r, --root</strong> rootname] [<strong>-w,--workingdir</strong> dirname] SDFile(s)...</p> | |
| 30 <p> | |
| 31 </p> | |
| 32 <h2>DESCRIPTION</h2> | |
| 33 <p>Split <em>SDFile(s)</em> into multiple SD files. Each new SDFile contains a compound | |
| 34 subset of similar size from the initial file. Multiple <em>SDFile(s)</em> names are separated | |
| 35 by space. The valid file extensions are <em>.sdf</em> and <em>.sd</em>. All other file names are | |
| 36 ignored. All the SD files in a current directory can be specified either by <em>*.sdf</em> | |
| 37 or the current directory name.</p> | |
| 38 <p> | |
| 39 </p> | |
| 40 <h2>OPTIONS</h2> | |
| 41 <dl> | |
| 42 <dt><strong><strong>-c, --CmpdsMode</strong> <em>DataField | MolName | RootPrefix</em></strong></dt> | |
| 43 <dd> | |
| 44 <p>This option is only used during <em>Cmpds</em> value of <-m, --mode> option with | |
| 45 specified <strong>--numcmpds</strong> value of 1.</p> | |
| 46 <p>Specify how to generate new file names during <em>Cmpds</em> value of <-m, --mode> | |
| 47 option: use <em>SDFile(s)</em> datafield value or molname line for a specific compound; | |
| 48 generate a sequential ID using root prefix specified by <strong>-r, --root</strong> option.</p> | |
| 49 <p>Possible values: <em>DataField | MolName | RootPrefix | RootPrefix</em>. | |
| 50 Default: <em>RootPrefix</em>.</p> | |
| 51 <p>For empty <em>MolName</em> and <em>DataField</em> values during these specified modes, file | |
| 52 name is automatically generated using <em>RootPrefix</em>.</p> | |
| 53 <p>For <em>RootPrefix</em> value of <strong>-c, --CmpdsMode</strong> option, new file names are | |
| 54 generated using by appending compound record number to value of <strong>-r, --root</strong> option. | |
| 55 For example: <em>RootName</em>Cmd<RecordNumber>.sdf.</p> | |
| 56 <p>Allowed characters in file names are: a-zA-Z0-9_. All other characters in datafield | |
| 57 values, molname line, and root prefix are ignore during generation of file names.</p> | |
| 58 </dd> | |
| 59 <dt><strong><strong>-d, --DataField</strong> <em>DataFieldName</em></strong></dt> | |
| 60 <dd> | |
| 61 <p>This option is only used during <em>DataField</em> value of <-c, --CmpdsMode> option.</p> | |
| 62 <p>Specify <em>SDFile(s)</em> datafield label name whose value is used for generation of new file | |
| 63 for a specific compound. Default value: <em>None</em>.</p> | |
| 64 </dd> | |
| 65 <dt><strong><strong>-h, --help</strong></strong></dt> | |
| 66 <dd> | |
| 67 <p>Print this help message.</p> | |
| 68 </dd> | |
| 69 <dt><strong><strong>-m, --mode</strong> <em>Cmpds | Files</em></strong></dt> | |
| 70 <dd> | |
| 71 <p>Specify how to split <em>SDFile(s)</em>: split into files with each file containing specified | |
| 72 number of compounds or split into a specified number of files.</p> | |
| 73 <p>Possible values: <em>Cmpds | Files</em>. Default: <em>Files</em>.</p> | |
| 74 <p>For <em>Cmpds</em> value of <strong>-m, --mode</strong> option, value of <strong>--numcmpds</strong> option | |
| 75 determines the number of new files. And value of <strong>-n, --numfiles</strong> option is | |
| 76 used to figure out the number of new files for <em>Files</em> value of <strong>-m, --mode</strong> option.</p> | |
| 77 </dd> | |
| 78 <dt><strong><strong>-n, --numfiles</strong> <em>number</em></strong></dt> | |
| 79 <dd> | |
| 80 <p>Number of new files to generate for each <em>SDFile(s)</em>. Default: <em>2</em>.</p> | |
| 81 <p>This value is only used during <em>Files</em> value of <strong>-m, --mode</strong> option.</p> | |
| 82 </dd> | |
| 83 <dt><strong><strong>--numcmpds</strong> <em>number</em></strong></dt> | |
| 84 <dd> | |
| 85 <p>Number of compounds in each new file corresponding to each <em>SDFile(s)</em>. | |
| 86 Default: <em>1</em>.</p> | |
| 87 <p>This value is only used during <em>Cmpds</em> value of <strong>-m, --mode</strong> option.</p> | |
| 88 </dd> | |
| 89 <dt><strong><strong>-o, --overwrite</strong></strong></dt> | |
| 90 <dd> | |
| 91 <p>Overwrite existing files.</p> | |
| 92 </dd> | |
| 93 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> | |
| 94 <dd> | |
| 95 <p>New SD file names are generated using the root: <Root>Part<Count>.sdf. | |
| 96 Default new file names: <InitialSDFileName> Part<Count>.sdf. This option | |
| 97 is ignored for multiple input files.</p> | |
| 98 </dd> | |
| 99 <dt><strong><strong>-w,--workingdir</strong> <em>dirname</em></strong></dt> | |
| 100 <dd> | |
| 101 <p>Location of working directory. Default: current directory.</p> | |
| 102 </dd> | |
| 103 </dl> | |
| 104 <p> | |
| 105 </p> | |
| 106 <h2>EXAMPLES</h2> | |
| 107 <p>To split each SD file into 5 new SD files, type:</p> | |
| 108 <div class="ExampleBox"> | |
| 109 % SplitSDFiles.pl -n 5 -o Sample1.sdf Sample2.sdf | |
| 110 <br/>% SplitSDFiles.pl -n 5 -o *.sdf</div> | |
| 111 <p>To split Sample1.sdf into 10 new NewSample*.sdf files, type:</p> | |
| 112 <div class="ExampleBox"> | |
| 113 % SplitSDFiles.pl -m Files -n 10 -r NewSample -o Sample1.sdf</div> | |
| 114 <p>To split Sample1.sdf into new NewSample*.sdf files containing maximum of 5 compounds | |
| 115 in each file, type:</p> | |
| 116 <div class="ExampleBox"> | |
| 117 % SplitSDFiles.pl -m Cmpds --numcmpds 5 -r NewSample -o Sample1.sdf</div> | |
| 118 <p>To split Sample1.sdf into new SD files containing one compound each with new file | |
| 119 names corresponding to molname line, type:</p> | |
| 120 <div class="ExampleBox"> | |
| 121 % SplitSDFiles.pl -m Cmpds --numcmpds 1 -c MolName -o Sample1.sdf</div> | |
| 122 <p>To split Sample1.sdf into new SD files containing one compound each with new file | |
| 123 names corresponding to value of datafield MolID, type:</p> | |
| 124 <div class="ExampleBox"> | |
| 125 % SplitSDFiles.pl -m Cmpds --numcmpds 1 -c DataField -d MolID | |
| 126 -o Sample1.sdf</div> | |
| 127 <p> | |
| 128 </p> | |
| 129 <h2>AUTHOR</h2> | |
| 130 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 131 <p> | |
| 132 </p> | |
| 133 <h2>SEE ALSO</h2> | |
| 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> | |
| 135 </p> | |
| 136 <p> | |
| 137 </p> | |
| 138 <h2>COPYRIGHT</h2> | |
| 139 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 140 <p>This file is part of MayaChemTools.</p> | |
| 141 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 142 the terms of the GNU Lesser General Public License as published by the Free | |
| 143 Software Foundation; either version 3 of the License, or (at your option) | |
| 144 any later version.</p> | |
| 145 <p> </p><p> </p><div class="DocNav"> | |
| 146 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 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> | |
| 148 </table> | |
| 149 </div> | |
| 150 <br /> | |
| 151 <center> | |
| 152 <img src="../../images/h2o2.png"> | |
| 153 </center> | |
| 154 </body> | |
| 155 </html> |