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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:ElementalAnalysisSDFiles.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="./ElementalAnalysis.html" title="ElementalAnalysis.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ElementalAnalysisTextFiles.html" title="ElementalAnalysisTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>ElementalAnalysisSDFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ElementalAnalysisSDFiles.html" title="View source code">Code</a> | <a href="./../pdf/ElementalAnalysisSDFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ElementalAnalysisSDFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ElementalAnalysisSDFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ElementalAnalysisSDFiles.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>ElementalAnalysisSDFiles.pl - Perform elemental analysis using formula data field in SDFile(s)</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>ElementalAnalysisSDFiles.pl SDFile(s)...</p> | |
| 26 <p>ElementalAnalysisSDFiles.pl [<strong>-d, --detail</strong> infolevel] [<strong>--fast</strong>] | |
| 27 [<strong>--formulafield</strong> SD data field name] [<strong>-f, --formulamode</strong> <em>DataField | StructureData</em>] | |
| 28 [<strong>--formulaout</strong> yes or no] [<strong>-m, --mode</strong> All | "ElementalAnalysis, [MolecularWeight, ExactMass]"] | |
| 29 [<strong>-h, --help</strong>] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] | |
| 30 [<strong>-v --valuefieldnames</strong> Name, Label, [Name, Label,...]] [<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p> | |
| 31 <p> | |
| 32 </p> | |
| 33 <h2>DESCRIPTION</h2> | |
| 34 <p>Perform elemental analysis using molecular formula specified by a data field name or generated | |
| 35 from structure data in <em>SDFile(s)</em>.</p> | |
| 36 <p>In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N - | |
| 37 other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O, | |
| 38 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including | |
| 39 D and T, are not supported.</p> | |
| 40 <p>The file names are separated by space.The valid file extensions are <em>.sdf</em> and <em>.sd</em>. | |
| 41 All other file names are ignored. All the SD files in a current directory can be specified | |
| 42 either by <em>*.sdf</em> or the current directory name.</p> | |
| 43 <p> | |
| 44 </p> | |
| 45 <h2>OPTIONS</h2> | |
| 46 <dl> | |
| 47 <dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt> | |
| 48 <dd> | |
| 49 <p>Level of information to print about compound records being ignored. Default: <em>1</em>. Possible | |
| 50 values: <em>1, 2 or 3</em>.</p> | |
| 51 </dd> | |
| 52 <dt><strong><strong>--fast</strong></strong></dt> | |
| 53 <dd> | |
| 54 <p>In this mode, the formula data field specified using <strong>-f, --formulafield</strong> option is assumed | |
| 55 to contain valid molecular formula data and initial formula validation check is skipped.</p> | |
| 56 </dd> | |
| 57 <dt><strong><strong>--formulafield</strong> <em>SD data field name</em></strong></dt> | |
| 58 <dd> | |
| 59 <p><em>SDFile(s)</em> data field name containing molecular formulas used for performing | |
| 60 elemental analysis during <em>DataField</em> value of <strong>-f, --formulamode</strong> option. | |
| 61 Default value: <em>SD data field containing the word formula in its name</em>.</p> | |
| 62 <p>This option is ignore during <em>StructureData</em> value of <strong>-f, --formulamode</strong> option.</p> | |
| 63 </dd> | |
| 64 <dt><strong><strong>-f, --formulamode</strong> <em>DataField | StructureData</em></strong></dt> | |
| 65 <dd> | |
| 66 <p>Specify source of molecular formula used for performing elemental analysis: retrieve | |
| 67 formula using <em>SDFile(s)</em> data field name or generate formula from structure. Possible | |
| 68 values: <em>DataField or StructureData</em>. Default value: <em>DataField</em>.</p> | |
| 69 </dd> | |
| 70 <dt><strong><strong>--formulaout</strong> <em>yes or no</em></strong></dt> | |
| 71 <dd> | |
| 72 <p>Specify whether to write out formula to SD file during <em>StructureData</em> value of | |
| 73 <strong>-f, --formulamode</strong> option. Possible values: <em>Yes or No</em>. Default: <em>No</em>.</p> | |
| 74 </dd> | |
| 75 <dt><strong><strong>-m, --mode</strong> <em>All | "ElementalAnalysis,[MolecularWeight,ExactMass]"</em></strong></dt> | |
| 76 <dd> | |
| 77 <p>Specify what values to calculate using molecular formula data field or structure data from | |
| 78 <em>SDFile(s)</em>: calculate all supported values or specify a comma delimited list of values. | |
| 79 Possible values: <em>All | "ElementalAnalysis, [MolecularWeight, ExactMass]"</em>. Default: <em>All</em></p> | |
| 80 </dd> | |
| 81 <dt><strong><strong>-h, --help</strong></strong></dt> | |
| 82 <dd> | |
| 83 <p>Print this help message.</p> | |
| 84 </dd> | |
| 85 <dt><strong><strong>-o, --overwrite</strong></strong></dt> | |
| 86 <dd> | |
| 87 <p>Overwrite existing files.</p> | |
| 88 </dd> | |
| 89 <dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt> | |
| 90 <dd> | |
| 91 <p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places. | |
| 92 Valid values: positive integers.</p> | |
| 93 </dd> | |
| 94 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> | |
| 95 <dd> | |
| 96 <p>New SD file name is generated using the root: <Root>.<Ext>. Default new file | |
| 97 name: <InitialSDFileName>ElementalAnalysis.<Ext>. This option is ignored for multiple | |
| 98 input files.</p> | |
| 99 </dd> | |
| 100 <dt><strong><strong>-v --valuefieldnames</strong> <em>Name,Label,[Name,Label,...]</em></strong></dt> | |
| 101 <dd> | |
| 102 <p>Specify SD data field names to use for calculated values. In general, it's a comma delimited | |
| 103 list of value name and SD field name pairs. Supported value names: <em>ElementalAnalysis, | |
| 104 MolecularWeight, ExactMass, and MolecularFormula</em>. Default labels: <em>ElementalAnalysis, | |
| 105 MolecularWeight, ExactMass, and MolecularFormula</em>.</p> | |
| 106 <p><em>MolecularFormula</em> label is only used during <em>StructureData</em> value of | |
| 107 <strong>-f, --formulamode</strong> option.</p> | |
| 108 </dd> | |
| 109 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> | |
| 110 <dd> | |
| 111 <p>Location of working directory. Default: current directory.</p> | |
| 112 </dd> | |
| 113 </dl> | |
| 114 <p> | |
| 115 </p> | |
| 116 <h2>EXAMPLES</h2> | |
| 117 <p>To perform elemental analysis, calculate molecular weight and exact mass using SD | |
| 118 field name value with the word Formula in its name and generate a new SD file | |
| 119 NewSample1.sdf, type:</p> | |
| 120 <div class="ExampleBox"> | |
| 121 % ElementalAnalysisSDFiles.pl -o -r NewSample1 Sample1.sdf</div> | |
| 122 <p>To perform elemental analysis, calculate molecular weight and exact mass using | |
| 123 structure data in SD file and generate a new SD file NewSample1.sdf, type:</p> | |
| 124 <div class="ExampleBox"> | |
| 125 % ElementalAnalysisSDFiles.pl --formulamode StructureData -o | |
| 126 -r NewSample1 Sample1.sdf</div> | |
| 127 <p>To perform elemental analysis using formulas in SD field name Formula, use field name | |
| 128 Analysis for calculated data, and generate a new SD file NewSample1.sdf, type:</p> | |
| 129 <div class="ExampleBox"> | |
| 130 % ElementalAnalysisSDFiles.pl --m ElementalAnalysis --formulafield | |
| 131 Formula --valuefieldnames "ElementalAnalysis,Analysis" -o | |
| 132 -r NewSample1 Sample1.sdf</div> | |
| 133 <p>To calculate molecular weight, using formulas in SD field name Formula, with four decimal | |
| 134 precision and generate a new SD file NewSample1.sdf, type</p> | |
| 135 <div class="ExampleBox"> | |
| 136 % ElementalAnalysisSDFiles.pl --m MolecularWeight --formulafield | |
| 137 Formula --precision 4 -o -r NewSample1 Sample1.sdf</div> | |
| 138 <p> | |
| 139 </p> | |
| 140 <h2>AUTHOR</h2> | |
| 141 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 142 <p> | |
| 143 </p> | |
| 144 <h2>SEE ALSO</h2> | |
| 145 <p><a href="./AnalyzeSDFilesData.html">AnalyzeSDFilesData.pl</a>, <a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./ExtractFromSDFiles.html">ExtractFromSDFiles.pl</a> | |
| 146 </p> | |
| 147 <p> | |
| 148 </p> | |
| 149 <h2>COPYRIGHT</h2> | |
| 150 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 151 <p>This file is part of MayaChemTools.</p> | |
| 152 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 153 the terms of the GNU Lesser General Public License as published by the Free | |
| 154 Software Foundation; either version 3 of the License, or (at your option) | |
| 155 any later version.</p> | |
| 156 <p> </p><p> </p><div class="DocNav"> | |
| 157 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 158 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysis.html" title="ElementalAnalysis.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ElementalAnalysisTextFiles.html" title="ElementalAnalysisTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ElementalAnalysisSDFiles.pl</strong></td></tr> | |
| 159 </table> | |
| 160 </div> | |
| 161 <br /> | |
| 162 <center> | |
| 163 <img src="../../images/h2o2.png"> | |
| 164 </center> | |
| 165 </body> | |
| 166 </html> |