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<html> <head> <title>MayaChemTools:Documentation:SDToMolFiles.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <p> </p> <h2>NAME</h2> <p>SDToMolFiles.pl - Generate MDLMOL file(s) from SD file(s)</p> <p> </p> <h2>SYNOPSIS</h2> <p>SDToMolFiles.pl SDFile(s)...</p> <p>SDToMolFiles.pl [<strong>-d, --DataField</strong> DataFieldName] [<strong>-m, --mode</strong> DataField | MolName | RootPrefix] [<strong>-h, --help</strong>] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] [<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p> <p> </p> <h2>DESCRIPTION</h2> <p>Generate MDLMOL file(s) from <em>SDFile(s)</em>. All header data labels and values in SDFile(s) are simply ignored; other appopriate data from SDFile(s) is transferred to MDLMOL files. Multiple <em>SDFile(s)</em> names are separated by spaces. The valid file extensions are <em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory can be specified either by <em>*.sdf</em> or the current directory name.</p> <p> </p> <h2>OPTIONS</h2> <dl> <dt><strong><strong>-d, --DataField</strong> <em>DataFieldName</em></strong></dt> <dd> <p>Specify <em>SDFile(s)</em> datafield label name whose value is used for generation of MDLMOL file names. Default value: <em>None</em>.</p> </dd> <dt><strong><strong>-h, --help</strong></strong></dt> <dd> <p>Print this help message.</p> </dd> <dt><strong><strong>-m, --mode</strong> <em>DataField | MolName | RootPrefix</em></strong></dt> <dd> <p>Specify how to generate MDLMOL file names: use a <em>SDFile(s)</em> datafield value; use molname line from <em>SDFile(s)</em>; generate a sequential ID using root prefix specified by <strong>-r, --root</strong> option.</p> <p>Possible values: <em>DataField | MolName | RootPrefix | RootPrefix</em>. Default: <em>RootPrefix</em>.</p> <p>For empty <em>MolName</em> and <em>DataField</em> values during these specified modes, file name is automatically generated using <em>RootPrefix</em>.</p> <p>For <em>RootPrefix</em> value of <strong>-m, --mode</strong> option, MDLMOL file names are generated using by appending compound record number to value of <strong>-r, --root</strong> option. For example: <em>RootName</em>Cmd<RecordNumber>.mol.</p> <p>Allowed characters in file names are: a-zA-Z0-9_. All other characters in datafield values, molname line, and root prefix are ignore during generation of file names.</p> </dd> <dt><strong><strong>-o, --overwrite</strong></strong></dt> <dd> <p>Overwrite existing files.</p> </dd> <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> <dd> <p>Specify root name to used during <em>RootPrefix</em> <strong>-m, --mode</strong> option value. New MDLMOL file names are generated using the root: <Root>Cmpd<RecordNumber>.mol Default for new file names: <InitialSDFileName>Cmpd<RecordNumber>.mol. This option is ignored for multiple input files.</p> </dd> <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> <dd> <p>Location of working directory. Default: current directory.</p> </dd> </dl> <p> </p> <h2>EXAMPLES</h2> <p>To generate MDLMOL files from Sample1*.sdf and Sample2*.sd files, type:</p> <div class="ExampleBox"> % SDToMolFiles.pl -o Sample1*.sdf Sample2*.sd</div> <p>To generate Sample*.mol files from Sample1.sdf, type:</p> <div class="ExampleBox"> % SDToMolFiles.pl -r Sample -o Sample1.sdf</div> <p>To generate MOL files from Sample1.sdf using molname line data for generating MOL file names, type:</p> <div class="ExampleBox"> % SDToMolFiles.pl -m MolName -r Sample -o Sample1.sdf</div> <p>To generate MOL files from Sample1.sdf using a specific data field values for generating MOL file names, type:</p> <div class="ExampleBox"> % SDToMolFiles.pl -m DataField --DataField MolID -r Sample -o Sample1.sdf</div> <p> </p> <h2>AUTHOR</h2> <p> </p> <h2>AUTHOR</h2> <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> <p> </p> <h2>SEE ALSO</h2> <p><a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./MolFilesToSD.html">MolFilesToSD.pl</a> </p> <p> </p> <h2>COPYRIGHT</h2> <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> <p>This file is part of MayaChemTools.</p> <p>MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.</p> <p> </p><p> </p><div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>