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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:InfoSDFiles.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="./InfoPeriodicTableElements.html" title="InfoPeriodicTableElements.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoSequenceFiles.html" title="InfoSequenceFiles.html">Next</a></td><td width="34%" align="middle"><strong>InfoSDFiles.pl</strong></td><td width="33%" align="right"><a href="././code/InfoSDFiles.html" title="View source code">Code</a> | <a href="./../pdf/InfoSDFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/InfoSDFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/InfoSDFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/InfoSDFiles.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>InfoSDFiles.pl - List information about SDFile(s)</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>InfoSDFile.pl SDFile(s)...</p> | |
| 26 <p>InfoSDFile.pl [<strong>-a --all</strong>] [<strong>-c --count</strong>] [<strong>--chiral</strong>] [<strong>--datacheck</strong>] | |
| 27 [<strong>-d --detail</strong> infolevel] [<strong>-e --empty</strong>] [<strong>-f, --fields</strong>] [<strong>-h, --help</strong>] | |
| 28 [<strong>-i, --invalidatomnumbers</strong>] [<strong>-m, --mismatch</strong>] [<strong>-s, --salts</strong>] [<strong>-u, --unknownatoms</strong>] | |
| 29 [<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p> | |
| 30 <p> | |
| 31 </p> | |
| 32 <h2>DESCRIPTION</h2> | |
| 33 <p>List information about <em>SDFile(s)</em> contents: number of compounds, empty records | |
| 34 and so on. Multiple SDFile names are separated by spaces. The valid file extensions | |
| 35 are <em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a current | |
| 36 directory can be specified either by <em>*.sdf</em> or the current directory name.</p> | |
| 37 <p> | |
| 38 </p> | |
| 39 <h2>OPTIONS</h2> | |
| 40 <dl> | |
| 41 <dt><strong><strong>-a, --all</strong></strong></dt> | |
| 42 <dd> | |
| 43 <p>List all the available information.</p> | |
| 44 </dd> | |
| 45 <dt><strong><strong>-c, --count</strong></strong></dt> | |
| 46 <dd> | |
| 47 <p>List number of compounds. This is <strong>default behavior</strong>.</p> | |
| 48 </dd> | |
| 49 <dt><strong><strong>--chiral</strong></strong></dt> | |
| 50 <dd> | |
| 51 <p>List number of empty atom/bond blocks for compounds with chiral flag set in | |
| 52 count line.</p> | |
| 53 </dd> | |
| 54 <dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt> | |
| 55 <dd> | |
| 56 <p>Level of information to print. Default: 1. Possible values: <em>1, 2, or 3</em>.</p> | |
| 57 </dd> | |
| 58 <dt><strong><strong>--datacheck</strong></strong></dt> | |
| 59 <dd> | |
| 60 <p>List number of numerical and non-numerical values for each data field.</p> | |
| 61 </dd> | |
| 62 <dt><strong><strong>-e, --empty</strong></strong></dt> | |
| 63 <dd> | |
| 64 <p>List number of empty atom/bond blocks and data fields for compounds.</p> | |
| 65 </dd> | |
| 66 <dt><strong><strong>-f, --fields</strong></strong></dt> | |
| 67 <dd> | |
| 68 <p>List data field labels present for compounds.</p> | |
| 69 </dd> | |
| 70 <dt><strong><strong>-h, --help</strong></strong></dt> | |
| 71 <dd> | |
| 72 <p>Print this help message.</p> | |
| 73 </dd> | |
| 74 <dt><strong><strong>-i, --invalidatomnumbers</strong></strong></dt> | |
| 75 <dd> | |
| 76 <p>List number of bond blocks for compounds which contain invalid atom numbers.</p> | |
| 77 </dd> | |
| 78 <dt><strong><strong>-m, --mismatch</strong></strong></dt> | |
| 79 <dd> | |
| 80 <p>List number of atom/bond blocks for compounds which don't match with counts | |
| 81 line information in header block.</p> | |
| 82 </dd> | |
| 83 <dt><strong><strong>-s, --salts</strong></strong></dt> | |
| 84 <dd> | |
| 85 <p>List number of atom blocks for compounds which contain salts identified as | |
| 86 disconnected structural units.</p> | |
| 87 </dd> | |
| 88 <dt><strong><strong>-u, --unknownatoms</strong></strong></dt> | |
| 89 <dd> | |
| 90 <p>List number of atom blocks for compounds which contain special atom symbols | |
| 91 such as L, Q, * ,LP, X, R#, or any other non periodic table symbols.</p> | |
| 92 </dd> | |
| 93 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> | |
| 94 <dd> | |
| 95 <p>Location of working directory. Default: current directory.</p> | |
| 96 </dd> | |
| 97 </dl> | |
| 98 <p> | |
| 99 </p> | |
| 100 <h2>EXAMPLES</h2> | |
| 101 <p>To count compounds in SD file(s), type:</p> | |
| 102 <div class="ExampleBox"> | |
| 103 % InfoSDFiles.pl Sample1.sdf | |
| 104 <br/>% InfoSDFiles.pl Sample1.sdf Sample2.sdf | |
| 105 <br/>% InfoSDFiles.pl *.sdf</div> | |
| 106 <p>To list all available information for SD file(s), type:</p> | |
| 107 <div class="ExampleBox"> | |
| 108 % InfoSDFiles.pl -a *.sdf</div> | |
| 109 <p>To list all data fields present in sample.sdf, type:</p> | |
| 110 <div class="ExampleBox"> | |
| 111 % InfoSDFiles.pl -f Sample.sdf</div> | |
| 112 <p>To count number of compounds which contain salts and list associated structural | |
| 113 data, type:</p> | |
| 114 <div class="ExampleBox"> | |
| 115 % InfoSDFiles.pl -s -d 3 Sample.sdf</div> | |
| 116 <p> | |
| 117 </p> | |
| 118 <h2>AUTHOR</h2> | |
| 119 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 120 <p> | |
| 121 </p> | |
| 122 <h2>SEE ALSO</h2> | |
| 123 <p><a href="./ExtractFromSDFiles.html">ExtractFromSDFiles.pl</a>, <a href="./FilterSDFiles.html">FilterSDFiles.pl</a>, <a href="./MergeTextFilesWithSD.html">MergeTextFilesWithSD.pl</a> | |
| 124 </p> | |
| 125 <p> | |
| 126 </p> | |
| 127 <h2>COPYRIGHT</h2> | |
| 128 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 129 <p>This file is part of MayaChemTools.</p> | |
| 130 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 131 the terms of the GNU Lesser General Public License as published by the Free | |
| 132 Software Foundation; either version 3 of the License, or (at your option) | |
| 133 any later version.</p> | |
| 134 <p> </p><p> </p><div class="DocNav"> | |
| 135 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 136 <tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoPeriodicTableElements.html" title="InfoPeriodicTableElements.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoSequenceFiles.html" title="InfoSequenceFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoSDFiles.pl</strong></td></tr> | |
| 137 </table> | |
| 138 </div> | |
| 139 <br /> | |
| 140 <center> | |
| 141 <img src="../../images/h2o2.png"> | |
| 142 </center> | |
| 143 </body> | |
| 144 </html> |