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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:MolFilesToSD.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="./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> | |
| 16 </table> | |
| 17 </div> | |
| 18 <p> | |
| 19 </p> | |
| 20 <h2>NAME</h2> | |
| 21 <p>MolFilesToSD.pl - Generate a SD file from MDLMOL File(s)</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>MolFilesToSD.pl MDLMOLFile(s)...</p> | |
| 26 <p>MolFilesToSD.pl [<strong>-c, --compoundid</strong> usefileprefix | idlabel] [<strong>-d, --datafieldlabel</strong> fieldlabel] | |
| 27 [<strong>-h, --help</strong>] [<strong>-m, --mode</strong> molnameline | datafield | both | none] [<strong>-o, --overwrite</strong>] | |
| 28 [<strong>-r, --root</strong> rootname] [<strong>-w, --workingdir</strong> dirname] MDLMOLFile(s)...</p> | |
| 29 <p> | |
| 30 </p> | |
| 31 <h2>DESCRIPTION</h2> | |
| 32 <p>Generate a SD file from <em>MDLMOL File(s)</em>. Multiple file names are separated by spaces. | |
| 33 The valid file extension is <em>.mol</em>. All other file names are ignored. All the files in a current | |
| 34 directory can be specified by <em>*.mol</em>, or the current directory name.</p> | |
| 35 <p> | |
| 36 </p> | |
| 37 <h2>OPTIONS</h2> | |
| 38 <dl> | |
| 39 <dt><strong><strong>-c, --compoundid</strong> <em>usefileprefix | idlabel</em></strong></dt> | |
| 40 <dd> | |
| 41 <p>Specify how to generate compound IDs: use MOL filename prefix or generate | |
| 42 a new compound ID by combining <em>idlabel</em> with compound number. Possible | |
| 43 values: <em>usefileprefix | idlabel</em>. By default, <em>Cmd</em> is used as a <em>idlabel</em> to generate | |
| 44 these types of compound IDs: Cmpd1, Cmpd2 and so on.</p> | |
| 45 <p>Example: To generate compound IDs like Mol_ID1, Mol_ID2 and so on, specify | |
| 46 "MolID" value for this option.</p> | |
| 47 </dd> | |
| 48 <dt><strong><strong>-d, --datafieldlabel</strong> <em>fieldlabel</em></strong></dt> | |
| 49 <dd> | |
| 50 <p>Specify data field label for adding compound ID field into SD file during <em>datafield | both</em> | |
| 51 values of <strong>-m, --mode</strong> option. Default: <Cmpd_ID>.</p> | |
| 52 </dd> | |
| 53 <dt><strong><strong>-h, --help</strong></strong></dt> | |
| 54 <dd> | |
| 55 <p>Print this help message.</p> | |
| 56 </dd> | |
| 57 <dt><strong><strong>-m, --mode</strong> <em>molnameline | datafield | both | none</em></strong></dt> | |
| 58 <dd> | |
| 59 <p>Specify how to add compopund ID into SD file: relplace the molname line, | |
| 60 add a new data field, replace the molname line and add data field, or do | |
| 61 nothing. Possible values: <em>molnameline | datafield | both | none</em>. | |
| 62 Default: <em>nothing</em>.</p> | |
| 63 <p>Use <strong>-c, --compoundid</strong> to specify compound ID generation process.</p> | |
| 64 </dd> | |
| 65 <dt><strong><strong>-o, --overwrite</strong></strong></dt> | |
| 66 <dd> | |
| 67 <p>Overwrite existing files.</p> | |
| 68 </dd> | |
| 69 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> | |
| 70 <dd> | |
| 71 <p>New SD file name is generated using the root: <Root>.sdf. Default new file | |
| 72 name: <InitialMOLFileName>1To<Count>.sdf.</p> | |
| 73 </dd> | |
| 74 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> | |
| 75 <dd> | |
| 76 <p>Location of working directory. Default: current directory.</p> | |
| 77 </dd> | |
| 78 </dl> | |
| 79 <p> | |
| 80 </p> | |
| 81 <h2>EXAMPLES</h2> | |
| 82 <p>To generate NewSample.sdf file from Sample*.mol files, type:</p> | |
| 83 <div class="ExampleBox"> | |
| 84 % MolFilesToSD.pl -r NewSample -o Sample*.mol</div> | |
| 85 <p>To generate NewSample.sdf with Cmpd1, Cmpd2 and so on as compound ID in | |
| 86 MolName line and Cmpd_ID datafield from Sample*.mol files, type:</p> | |
| 87 <div class="ExampleBox"> | |
| 88 % MolFilesToSD.pl -r NewSample -m both -o Sample*.mol</div> | |
| 89 <p> | |
| 90 </p> | |
| 91 <h2>AUTHOR</h2> | |
| 92 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 93 <p> | |
| 94 </p> | |
| 95 <h2>SEE ALSO</h2> | |
| 96 <p><a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./SDToMolFiles.html">SDToMolFiles.pl</a> | |
| 97 </p> | |
| 98 <p> | |
| 99 </p> | |
| 100 <h2>COPYRIGHT</h2> | |
| 101 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 102 <p>This file is part of MayaChemTools.</p> | |
| 103 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 104 the terms of the GNU Lesser General Public License as published by the Free | |
| 105 Software Foundation; either version 3 of the License, or (at your option) | |
| 106 any later version.</p> | |
| 107 <p> </p><p> </p><div class="DocNav"> | |
| 108 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 109 <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> | |
| 110 </table> | |
| 111 </div> | |
| 112 <br /> | |
| 113 <center> | |
| 114 <img src="../../images/h2o2.png"> | |
| 115 </center> | |
| 116 </body> | |
| 117 </html> |