Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/scripts/html/SplitSDFiles.html @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/html/SplitSDFiles.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,155 @@ +<html> +<head> +<title>MayaChemTools:Documentation:SplitSDFiles.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="./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> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>SplitSDFiles.pl - Split SDFile(s) into multiple SD files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>SplitSDFiles.pl SDFile(s)...</p> +<p>SplitSDFiles.pl [<strong>-c, --CmpdsMode</strong> DataField | MolName | RootPrefix] +[<strong>-d, --DataField</strong> DataFieldName] [<strong>-h, --help</strong>] [<strong>-m, --mode</strong> Cmpds | Files] +[<strong>-n, --numfiles</strong> number] [<strong>--numcmpds</strong> number] [<strong>-o, --overwrite</strong>] +[<strong>-r, --root</strong> rootname] [<strong>-w,--workingdir</strong> dirname] SDFile(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Split <em>SDFile(s)</em> into multiple SD files. Each new SDFile contains a compound +subset of similar size from the initial file. Multiple <em>SDFile(s)</em> names are separated +by space. 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>-c, --CmpdsMode</strong> <em>DataField | MolName | RootPrefix</em></strong></dt> +<dd> +<p>This option is only used during <em>Cmpds</em> value of <-m, --mode> option with +specified <strong>--numcmpds</strong> value of 1.</p> +<p>Specify how to generate new file names during <em>Cmpds</em> value of <-m, --mode> +option: use <em>SDFile(s)</em> datafield value or molname line for a specific compound; +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>-c, --CmpdsMode</strong> option, new 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>.sdf.</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>-d, --DataField</strong> <em>DataFieldName</em></strong></dt> +<dd> +<p>This option is only used during <em>DataField</em> value of <-c, --CmpdsMode> option.</p> +<p>Specify <em>SDFile(s)</em> datafield label name whose value is used for generation of new file +for a specific compound. 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>Cmpds | Files</em></strong></dt> +<dd> +<p>Specify how to split <em>SDFile(s)</em>: split into files with each file containing specified +number of compounds or split into a specified number of files.</p> +<p>Possible values: <em>Cmpds | Files</em>. Default: <em>Files</em>.</p> +<p>For <em>Cmpds</em> value of <strong>-m, --mode</strong> option, value of <strong>--numcmpds</strong> option +determines the number of new files. And value of <strong>-n, --numfiles</strong> option is +used to figure out the number of new files for <em>Files</em> value of <strong>-m, --mode</strong> option.</p> +</dd> +<dt><strong><strong>-n, --numfiles</strong> <em>number</em></strong></dt> +<dd> +<p>Number of new files to generate for each <em>SDFile(s)</em>. Default: <em>2</em>.</p> +<p>This value is only used during <em>Files</em> value of <strong>-m, --mode</strong> option.</p> +</dd> +<dt><strong><strong>--numcmpds</strong> <em>number</em></strong></dt> +<dd> +<p>Number of compounds in each new file corresponding to each <em>SDFile(s)</em>. +Default: <em>1</em>.</p> +<p>This value is only used during <em>Cmpds</em> value of <strong>-m, --mode</strong> option.</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 names are generated using the root: <Root>Part<Count>.sdf. +Default new file names: <InitialSDFileName> Part<Count>.sdf. 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 split each SD file into 5 new SD files, type:</p> +<div class="ExampleBox"> + % SplitSDFiles.pl -n 5 -o Sample1.sdf Sample2.sdf + <br/>% SplitSDFiles.pl -n 5 -o *.sdf</div> +<p>To split Sample1.sdf into 10 new NewSample*.sdf files, type:</p> +<div class="ExampleBox"> + % SplitSDFiles.pl -m Files -n 10 -r NewSample -o Sample1.sdf</div> +<p>To split Sample1.sdf into new NewSample*.sdf files containing maximum of 5 compounds +in each file, type:</p> +<div class="ExampleBox"> + % SplitSDFiles.pl -m Cmpds --numcmpds 5 -r NewSample -o Sample1.sdf</div> +<p>To split Sample1.sdf into new SD files containing one compound each with new file +names corresponding to molname line, type:</p> +<div class="ExampleBox"> + % SplitSDFiles.pl -m Cmpds --numcmpds 1 -c MolName -o Sample1.sdf</div> +<p>To split Sample1.sdf into new SD files containing one compound each with new file +names corresponding to value of datafield MolID, type:</p> +<div class="ExampleBox"> + % SplitSDFiles.pl -m Cmpds --numcmpds 1 -c DataField -d MolID + -o Sample1.sdf</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="./JoinSDFiles.html">JoinSDFiles.pl</a>, <a href="./MolFilesToSD.html">MolFilesToSD.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="./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> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>