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<html> <head> <title>MayaChemTools:Documentation:ElementalAnalysisSDFiles.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <p> </p> <h2>NAME</h2> <p>ElementalAnalysisSDFiles.pl - Perform elemental analysis using formula data field in SDFile(s)</p> <p> </p> <h2>SYNOPSIS</h2> <p>ElementalAnalysisSDFiles.pl SDFile(s)...</p> <p>ElementalAnalysisSDFiles.pl [<strong>-d, --detail</strong> infolevel] [<strong>--fast</strong>] [<strong>--formulafield</strong> SD data field name] [<strong>-f, --formulamode</strong> <em>DataField | StructureData</em>] [<strong>--formulaout</strong> yes or no] [<strong>-m, --mode</strong> All | "ElementalAnalysis, [MolecularWeight, ExactMass]"] [<strong>-h, --help</strong>] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] [<strong>-v --valuefieldnames</strong> Name, Label, [Name, Label,...]] [<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p> <p> </p> <h2>DESCRIPTION</h2> <p>Perform elemental analysis using molecular formula specified by a data field name or generated from structure data in <em>SDFile(s)</em>.</p> <p>In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N - other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O, 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including D and T, are not supported.</p> <p>The file names are separated by space.The valid file extensions are <em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory can be specified either by <em>*.sdf</em> or the current directory name.</p> <p> </p> <h2>OPTIONS</h2> <dl> <dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt> <dd> <p>Level of information to print about compound records being ignored. Default: <em>1</em>. Possible values: <em>1, 2 or 3</em>.</p> </dd> <dt><strong><strong>--fast</strong></strong></dt> <dd> <p>In this mode, the formula data field specified using <strong>-f, --formulafield</strong> option is assumed to contain valid molecular formula data and initial formula validation check is skipped.</p> </dd> <dt><strong><strong>--formulafield</strong> <em>SD data field name</em></strong></dt> <dd> <p><em>SDFile(s)</em> data field name containing molecular formulas used for performing elemental analysis during <em>DataField</em> value of <strong>-f, --formulamode</strong> option. Default value: <em>SD data field containing the word formula in its name</em>.</p> <p>This option is ignore during <em>StructureData</em> value of <strong>-f, --formulamode</strong> option.</p> </dd> <dt><strong><strong>-f, --formulamode</strong> <em>DataField | StructureData</em></strong></dt> <dd> <p>Specify source of molecular formula used for performing elemental analysis: retrieve formula using <em>SDFile(s)</em> data field name or generate formula from structure. Possible values: <em>DataField or StructureData</em>. Default value: <em>DataField</em>.</p> </dd> <dt><strong><strong>--formulaout</strong> <em>yes or no</em></strong></dt> <dd> <p>Specify whether to write out formula to SD file during <em>StructureData</em> value of <strong>-f, --formulamode</strong> option. Possible values: <em>Yes or No</em>. Default: <em>No</em>.</p> </dd> <dt><strong><strong>-m, --mode</strong> <em>All | "ElementalAnalysis,[MolecularWeight,ExactMass]"</em></strong></dt> <dd> <p>Specify what values to calculate using molecular formula data field or structure data from <em>SDFile(s)</em>: calculate all supported values or specify a comma delimited list of values. Possible values: <em>All | "ElementalAnalysis, [MolecularWeight, ExactMass]"</em>. Default: <em>All</em></p> </dd> <dt><strong><strong>-h, --help</strong></strong></dt> <dd> <p>Print this help message.</p> </dd> <dt><strong><strong>-o, --overwrite</strong></strong></dt> <dd> <p>Overwrite existing files.</p> </dd> <dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt> <dd> <p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places. Valid values: positive integers.</p> </dd> <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> <dd> <p>New SD file name is generated using the root: <Root>.<Ext>. Default new file name: <InitialSDFileName>ElementalAnalysis.<Ext>. This option is ignored for multiple input files.</p> </dd> <dt><strong><strong>-v --valuefieldnames</strong> <em>Name,Label,[Name,Label,...]</em></strong></dt> <dd> <p>Specify SD data field names to use for calculated values. In general, it's a comma delimited list of value name and SD field name pairs. Supported value names: <em>ElementalAnalysis, MolecularWeight, ExactMass, and MolecularFormula</em>. Default labels: <em>ElementalAnalysis, MolecularWeight, ExactMass, and MolecularFormula</em>.</p> <p><em>MolecularFormula</em> label is only used during <em>StructureData</em> value of <strong>-f, --formulamode</strong> option.</p> </dd> <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> <dd> <p>Location of working directory. Default: current directory.</p> </dd> </dl> <p> </p> <h2>EXAMPLES</h2> <p>To perform elemental analysis, calculate molecular weight and exact mass using SD field name value with the word Formula in its name and generate a new SD file NewSample1.sdf, type:</p> <div class="ExampleBox"> % ElementalAnalysisSDFiles.pl -o -r NewSample1 Sample1.sdf</div> <p>To perform elemental analysis, calculate molecular weight and exact mass using structure data in SD file and generate a new SD file NewSample1.sdf, type:</p> <div class="ExampleBox"> % ElementalAnalysisSDFiles.pl --formulamode StructureData -o -r NewSample1 Sample1.sdf</div> <p>To perform elemental analysis using formulas in SD field name Formula, use field name Analysis for calculated data, and generate a new SD file NewSample1.sdf, type:</p> <div class="ExampleBox"> % ElementalAnalysisSDFiles.pl --m ElementalAnalysis --formulafield Formula --valuefieldnames "ElementalAnalysis,Analysis" -o -r NewSample1 Sample1.sdf</div> <p>To calculate molecular weight, using formulas in SD field name Formula, with four decimal precision and generate a new SD file NewSample1.sdf, type</p> <div class="ExampleBox"> % ElementalAnalysisSDFiles.pl --m MolecularWeight --formulafield Formula --precision 4 -o -r NewSample1 Sample1.sdf</div> <p> </p> <h2>AUTHOR</h2> <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> <p> </p> <h2>SEE ALSO</h2> <p><a href="./AnalyzeSDFilesData.html">AnalyzeSDFilesData.pl</a>, <a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./ExtractFromSDFiles.html">ExtractFromSDFiles.pl</a> </p> <p> </p> <h2>COPYRIGHT</h2> <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> <p>This file is part of MayaChemTools.</p> <p>MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.</p> <p> </p><p> </p><div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>