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<p>
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<h2>NAME</h2>
<p>ElementalAnalysis.pl - Perform elemental analysis using specified formulas</p>
<p>
</p>
<h2>SYNOPSIS</h2>
<p>ElementalAnalysis.pl Formula(s)...</p>
<p>ElementalAnalysis.pl [<strong>-h, --help</strong>]
[<strong>-m, --mode</strong> All | &quot;ElementalAnalysis, [MolecularWeight, ExactMass]&quot;]
[<strong>--outdelim</strong> comma | tab | semicolon]
[<strong>--output</strong> STDOUT | File] [<strong>--outputstyle</strong> FormulaBlock | FormulaRows]
[<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname]
[<strong>-v --valuelabels</strong> [Name, Label, [Name, Label,...]]
[<strong>-w, --workingdir</strong> dirname] Formula(s)...</p>
<p>
</p>
<h2>DESCRIPTION</h2>
<p>Perform elemental analysis using molecular formula(s) specified on the command line.</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>
</p>
<h2>PARAMETERS</h2>
<dl>
<dt><strong><strong>Formulas</strong> <em>Formula1 [Formula2...]</em></strong></dt>
<dd>
<p><em>Formulas</em> is a space delimited list of molecular formulas to use for elemental analysis.</p>
<p>Input value format is: <em>Formula1 [Formula2 Formula3...]</em>. Default: <em>H2O</em>.
Examples:</p>
<div class="OptionsBox">
    HCl
<br/>    HCl, C3H7O2N
<br/>    H2O2 Ca3(PO4)2 [PCl4]+</div>
</dd>
</dl>
<p>
</p>
<h2>OPTIONS</h2>
<dl>
<dt><strong><strong>-h, --help</strong></strong></dt>
<dd>
<p>Print this help message.</p>
</dd>
<dt><strong><strong>--fast</strong></strong></dt>
<dd>
<p>In this mode, the specified formulas are considered valid and initial formula
validation check is skipped.</p>
</dd>
<dt><strong><strong>-m, --mode</strong> <em>All | &quot;ElementalAnalysis,[MolecularWeight,ExactMass]&quot;</em></strong></dt>
<dd>
<p>Specify what values to calculate using molecular formulas specified on command
line: calculate all supported values or specify a comma delimited list of values. Possible
values: <em>All | &quot;ElementalAnalysis, [MolecularWeight, ExactMass]&quot;</em>. Default: <em>All</em>.</p>
</dd>
<dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt>
<dd>
<p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>
Default value: <em>comma</em>.</p>
</dd>
<dt><strong><strong>--output</strong> <em>STDOUT | File</em></strong></dt>
<dd>
<p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default:
<em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p>
</dd>
<dt><strong><strong>--outputstyle</strong> <em>FormulaBlock | FormulaRows</em></strong></dt>
<dd>
<p>Specify how to list calculated values: add a new line for each property and present it as a block
for each formula; or include all properties in one line and show it as a single line.</p>
<p>Possible values: <em>FormulaBlock | FormulaRows</em>. Default: <em>FormulaBlock</em></p>
<p>An example for <em>FormulaBlock</em> output style:</p>
<div class="OptionsBox">
    Formula: H2O
<br/>    ElementalAnalysis: H: H: 11.1898%; O: 88.8102%
<br/>    MolecularWeight: 18.0153
<br/>    ExactMass: 18.0106
<br/>    ... ...
<br/>    ... ...
<br/>    ... ...</div>
<div class="OptionsBox">
    Formula: H2O2
<br/>    ElementalAnalysis: H: 5.9265%; O: 94.0735%
<br/>    MolecularWeight: 34.0147
<br/>    ExactMass: 34.0055
<br/>    ... ...
<br/>    ... ...
<br/>    ... ...</div>
<p>An example for <em>FormulaRows</em> output style:</p>
<div class="OptionsBox">
    Formula,ElementalAnalysis,MolecularWeight,ExactMass
<br/>    H2O,H: 11.1898%; O: 88.8102%,18.0153,18.0106
<br/>    H2O2,H: 5.9265%; O: 94.0735%,34.0147,34.0055</div>
</dd>
<dt><strong><strong>-o, --overwrite</strong></strong></dt>
<dd>
<p>Overwrite existing files.</p>
</dd>
<dt><strong><strong>--precision</strong> <em>number</em></strong></dt>
<dd>
<p>Precision for listing numerical values. Default: up to <em>4</em> decimal places.
Valid values: positive integers.</p>
</dd>
<dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
<dd>
<p>New text file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. File name is only
used during <em>File</em> value of <strong>-o, --output</strong> option.</p>
<p>Default file name: FormulsElementalAnalysis.&lt;Ext&gt;. The csv, and tsv
&lt;Ext&gt; values are used for comma/semicolon, and tab delimited text files respectively.</p>
</dd>
<dt><strong><strong>-v --valuelabels</strong> <em>Name,Label,[Name,Label,...]</em></strong></dt>
<dd>
<p>Specify labels to use for calculated values. In general, it's a comma delimited
list of value name and column label pairs. Supported value names: <em>ElementalAnalysis,
MolecularWeight,  and ExactMass</em>. Default labels: <em>ElementalAnalysis, MolecularWeight,
and ExactMass</em>.</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 for H2O,
type:</p>
<div class="ExampleBox">
    % ElementalAnalysis.pl</div>
<p>To perform elemental analysis, calculate molecular weight and exact mass for
Ca3(PO4)2 and [PCl4]+, type:</p>
<div class="ExampleBox">
    % ElementalAnalysis.pl &quot;Ca3(PO4)2&quot; &quot;[PCl4]+&quot;</div>
<p>To perform elemental analysis, use label analysis for calculated data, and generate a
new CSV file ElementalAnalysis.csv for H2O and H2O2, type:</p>
<div class="ExampleBox">
    % ElementalAnalysis.pl --m ElementalAnalysis --output File
      --valuelabels &quot;ElementalAnalysis,Analysis&quot; -o -r ElementalAnalysis.csv
      H2O H2O2</div>
<p>To calculate molecular weight and exact mass with four decimal precision and
generate a new CSV file WeightAndMass.csv with data rows for H2O and H2O2, type:</p>
<div class="ExampleBox">
    % ElementalAnalysis.pl --m &quot;MolecularWeight,ExactMass&quot; --output File
      --outputstyle FormulaRows -o -r WeightAndMass.csv
      H2O H2O2</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="./ElementalAnalysisSDFiles.html">ElementalAnalysisSDFiles.pl</a>,&nbsp<a href="./ElementalAnalysisTextFiles.html">ElementalAnalysisTextFiles.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>
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