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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/SDToMolFiles.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,131 @@ +<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>