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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/MolFilesToSD.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,117 @@ +<html> +<head> +<title>MayaChemTools:Documentation:MolFilesToSD.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="./ModifyTextFilesFormat.html" title="ModifyTextFilesFormat.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>MolFilesToSD.pl</strong></td><td width="33%" align="right"><a href="././code/MolFilesToSD.html" title="View source code">Code</a> | <a href="./../pdf/MolFilesToSD.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MolFilesToSD.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MolFilesToSD.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MolFilesToSD.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>MolFilesToSD.pl - Generate a SD file from MDLMOL File(s)</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>MolFilesToSD.pl MDLMOLFile(s)...</p> +<p>MolFilesToSD.pl [<strong>-c, --compoundid</strong> usefileprefix | idlabel] [<strong>-d, --datafieldlabel</strong> fieldlabel] +[<strong>-h, --help</strong>] [<strong>-m, --mode</strong> molnameline | datafield | both | none] [<strong>-o, --overwrite</strong>] +[<strong>-r, --root</strong> rootname] [<strong>-w, --workingdir</strong> dirname] MDLMOLFile(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Generate a SD file from <em>MDLMOL File(s)</em>. Multiple file names are separated by spaces. +The valid file extension is <em>.mol</em>. All other file names are ignored. All the files in a current +directory can be specified by <em>*.mol</em>, or the current directory name.</p> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>-c, --compoundid</strong> <em>usefileprefix | idlabel</em></strong></dt> +<dd> +<p>Specify how to generate compound IDs: use MOL filename prefix or generate +a new compound ID by combining <em>idlabel</em> with compound number. Possible +values: <em>usefileprefix | idlabel</em>. By default, <em>Cmd</em> is used as a <em>idlabel</em> to generate +these types of compound IDs: Cmpd1, Cmpd2 and so on.</p> +<p>Example: To generate compound IDs like Mol_ID1, Mol_ID2 and so on, specify +"MolID" value for this option.</p> +</dd> +<dt><strong><strong>-d, --datafieldlabel</strong> <em>fieldlabel</em></strong></dt> +<dd> +<p>Specify data field label for adding compound ID field into SD file during <em>datafield | both</em> +values of <strong>-m, --mode</strong> option. Default: <Cmpd_ID>.</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>molnameline | datafield | both | none</em></strong></dt> +<dd> +<p>Specify how to add compopund ID into SD file: relplace the molname line, +add a new data field, replace the molname line and add data field, or do +nothing. Possible values: <em>molnameline | datafield | both | none</em>. +Default: <em>nothing</em>.</p> +<p>Use <strong>-c, --compoundid</strong> to specify compound ID generation process.</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>New SD file name is generated using the root: <Root>.sdf. Default new file +name: <InitialMOLFileName>1To<Count>.sdf.</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 NewSample.sdf file from Sample*.mol files, type:</p> +<div class="ExampleBox"> + % MolFilesToSD.pl -r NewSample -o Sample*.mol</div> +<p>To generate NewSample.sdf with Cmpd1, Cmpd2 and so on as compound ID in +MolName line and Cmpd_ID datafield from Sample*.mol files, type:</p> +<div class="ExampleBox"> + % MolFilesToSD.pl -r NewSample -m both -o Sample*.mol</div> +<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="./SDToMolFiles.html">SDToMolFiles.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="./ModifyTextFilesFormat.html" title="ModifyTextFilesFormat.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolFilesToSD.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>