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