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comparison mayachemtools/docs/scripts/html/SDToMolFiles.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| -1:000000000000 | 0:73ae111cf86f |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:SDToMolFiles.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="./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> | |
| 16 </table> | |
| 17 </div> | |
| 18 <p> | |
| 19 </p> | |
| 20 <h2>NAME</h2> | |
| 21 <p>SDToMolFiles.pl - Generate MDLMOL file(s) from SD file(s)</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>SDToMolFiles.pl SDFile(s)...</p> | |
| 26 <p>SDToMolFiles.pl [<strong>-d, --DataField</strong> DataFieldName] | |
| 27 [<strong>-m, --mode</strong> DataField | MolName | RootPrefix] [<strong>-h, --help</strong>] | |
| 28 [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] | |
| 29 [<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p> | |
| 30 <p> | |
| 31 </p> | |
| 32 <h2>DESCRIPTION</h2> | |
| 33 <p>Generate MDLMOL file(s) from <em>SDFile(s)</em>. All header data labels and values in | |
| 34 SDFile(s) are simply ignored; other appopriate data from SDFile(s) is transferred to MDLMOL | |
| 35 files. Multiple <em>SDFile(s)</em> names are separated by spaces. The valid file extensions are | |
| 36 <em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a current | |
| 37 directory can be specified either by <em>*.sdf</em> or the current directory name.</p> | |
| 38 <p> | |
| 39 </p> | |
| 40 <h2>OPTIONS</h2> | |
| 41 <dl> | |
| 42 <dt><strong><strong>-d, --DataField</strong> <em>DataFieldName</em></strong></dt> | |
| 43 <dd> | |
| 44 <p>Specify <em>SDFile(s)</em> datafield label name whose value is used for generation of MDLMOL | |
| 45 file names. Default value: <em>None</em>.</p> | |
| 46 </dd> | |
| 47 <dt><strong><strong>-h, --help</strong></strong></dt> | |
| 48 <dd> | |
| 49 <p>Print this help message.</p> | |
| 50 </dd> | |
| 51 <dt><strong><strong>-m, --mode</strong> <em>DataField | MolName | RootPrefix</em></strong></dt> | |
| 52 <dd> | |
| 53 <p>Specify how to generate MDLMOL file names: use a <em>SDFile(s)</em> datafield value; use | |
| 54 molname line from <em>SDFile(s)</em>; generate a sequential ID using root prefix specified | |
| 55 by <strong>-r, --root</strong> option.</p> | |
| 56 <p>Possible values: <em>DataField | MolName | RootPrefix | RootPrefix</em>. | |
| 57 Default: <em>RootPrefix</em>.</p> | |
| 58 <p>For empty <em>MolName</em> and <em>DataField</em> values during these specified modes, file | |
| 59 name is automatically generated using <em>RootPrefix</em>.</p> | |
| 60 <p>For <em>RootPrefix</em> value of <strong>-m, --mode</strong> option, MDLMOL file names are generated | |
| 61 using by appending compound record number to value of <strong>-r, --root</strong> option. For | |
| 62 example: <em>RootName</em>Cmd<RecordNumber>.mol.</p> | |
| 63 <p>Allowed characters in file names are: a-zA-Z0-9_. All other characters in datafield | |
| 64 values, molname line, and root prefix are ignore during generation of file names.</p> | |
| 65 </dd> | |
| 66 <dt><strong><strong>-o, --overwrite</strong></strong></dt> | |
| 67 <dd> | |
| 68 <p>Overwrite existing files.</p> | |
| 69 </dd> | |
| 70 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> | |
| 71 <dd> | |
| 72 <p>Specify root name to used during <em>RootPrefix</em> <strong>-m, --mode</strong> option value. | |
| 73 New MDLMOL file names are generated using the root: <Root>Cmpd<RecordNumber>.mol | |
| 74 Default for new file names: <InitialSDFileName>Cmpd<RecordNumber>.mol. This option | |
| 75 is ignored for multiple input files.</p> | |
| 76 </dd> | |
| 77 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> | |
| 78 <dd> | |
| 79 <p>Location of working directory. Default: current directory.</p> | |
| 80 </dd> | |
| 81 </dl> | |
| 82 <p> | |
| 83 </p> | |
| 84 <h2>EXAMPLES</h2> | |
| 85 <p>To generate MDLMOL files from Sample1*.sdf and Sample2*.sd files, type:</p> | |
| 86 <div class="ExampleBox"> | |
| 87 % SDToMolFiles.pl -o Sample1*.sdf Sample2*.sd</div> | |
| 88 <p>To generate Sample*.mol files from Sample1.sdf, type:</p> | |
| 89 <div class="ExampleBox"> | |
| 90 % SDToMolFiles.pl -r Sample -o Sample1.sdf</div> | |
| 91 <p>To generate MOL files from Sample1.sdf using molname line data for generating | |
| 92 MOL file names, type:</p> | |
| 93 <div class="ExampleBox"> | |
| 94 % SDToMolFiles.pl -m MolName -r Sample -o Sample1.sdf</div> | |
| 95 <p>To generate MOL files from Sample1.sdf using a specific data field values for | |
| 96 generating MOL file names, type:</p> | |
| 97 <div class="ExampleBox"> | |
| 98 % SDToMolFiles.pl -m DataField --DataField MolID -r Sample | |
| 99 -o Sample1.sdf</div> | |
| 100 <p> | |
| 101 </p> | |
| 102 <h2>AUTHOR</h2> | |
| 103 <p> | |
| 104 </p> | |
| 105 <h2>AUTHOR</h2> | |
| 106 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 107 <p> | |
| 108 </p> | |
| 109 <h2>SEE ALSO</h2> | |
| 110 <p><a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./MolFilesToSD.html">MolFilesToSD.pl</a> | |
| 111 </p> | |
| 112 <p> | |
| 113 </p> | |
| 114 <h2>COPYRIGHT</h2> | |
| 115 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 116 <p>This file is part of MayaChemTools.</p> | |
| 117 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 118 the terms of the GNU Lesser General Public License as published by the Free | |
| 119 Software Foundation; either version 3 of the License, or (at your option) | |
| 120 any later version.</p> | |
| 121 <p> </p><p> </p><div class="DocNav"> | |
| 122 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 123 <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> | |
| 124 </table> | |
| 125 </div> | |
| 126 <br /> | |
| 127 <center> | |
| 128 <img src="../../images/h2o2.png"> | |
| 129 </center> | |
| 130 </body> | |
| 131 </html> |