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3 <title>MayaChemTools:Documentation:ElementalAnalysis.pl</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./DBTablesToTextFiles.html" title="DBTablesToTextFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./ElementalAnalysisSDFiles.html" title="ElementalAnalysisSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>ElementalAnalysis.pl</strong></td><td width="33%" align="right"><a href="././code/ElementalAnalysis.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/ElementalAnalysis.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/ElementalAnalysis.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/ElementalAnalysis.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/ElementalAnalysis.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>ElementalAnalysis.pl - Perform elemental analysis using specified formulas</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>ElementalAnalysis.pl Formula(s)...</p>
26 <p>ElementalAnalysis.pl [<strong>-h, --help</strong>]
27 [<strong>-m, --mode</strong> All | &quot;ElementalAnalysis, [MolecularWeight, ExactMass]&quot;]
28 [<strong>--outdelim</strong> comma | tab | semicolon]
29 [<strong>--output</strong> STDOUT | File] [<strong>--outputstyle</strong> FormulaBlock | FormulaRows]
30 [<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname]
31 [<strong>-v --valuelabels</strong> [Name, Label, [Name, Label,...]]
32 [<strong>-w, --workingdir</strong> dirname] Formula(s)...</p>
33 <p>
34 </p>
35 <h2>DESCRIPTION</h2>
36 <p>Perform elemental analysis using molecular formula(s) specified on the command line.</p>
37 <p>In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
38 other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O,
39 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
40 D and T, are not supported.</p>
41 <p>
42 </p>
43 <h2>PARAMETERS</h2>
44 <dl>
45 <dt><strong><strong>Formulas</strong> <em>Formula1 [Formula2...]</em></strong></dt>
46 <dd>
47 <p><em>Formulas</em> is a space delimited list of molecular formulas to use for elemental analysis.</p>
48 <p>Input value format is: <em>Formula1 [Formula2 Formula3...]</em>. Default: <em>H2O</em>.
49 Examples:</p>
50 <div class="OptionsBox">
51 HCl
52 <br/> HCl, C3H7O2N
53 <br/> H2O2 Ca3(PO4)2 [PCl4]+</div>
54 </dd>
55 </dl>
56 <p>
57 </p>
58 <h2>OPTIONS</h2>
59 <dl>
60 <dt><strong><strong>-h, --help</strong></strong></dt>
61 <dd>
62 <p>Print this help message.</p>
63 </dd>
64 <dt><strong><strong>--fast</strong></strong></dt>
65 <dd>
66 <p>In this mode, the specified formulas are considered valid and initial formula
67 validation check is skipped.</p>
68 </dd>
69 <dt><strong><strong>-m, --mode</strong> <em>All | &quot;ElementalAnalysis,[MolecularWeight,ExactMass]&quot;</em></strong></dt>
70 <dd>
71 <p>Specify what values to calculate using molecular formulas specified on command
72 line: calculate all supported values or specify a comma delimited list of values. Possible
73 values: <em>All | &quot;ElementalAnalysis, [MolecularWeight, ExactMass]&quot;</em>. Default: <em>All</em>.</p>
74 </dd>
75 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt>
76 <dd>
77 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>
78 Default value: <em>comma</em>.</p>
79 </dd>
80 <dt><strong><strong>--output</strong> <em>STDOUT | File</em></strong></dt>
81 <dd>
82 <p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default:
83 <em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p>
84 </dd>
85 <dt><strong><strong>--outputstyle</strong> <em>FormulaBlock | FormulaRows</em></strong></dt>
86 <dd>
87 <p>Specify how to list calculated values: add a new line for each property and present it as a block
88 for each formula; or include all properties in one line and show it as a single line.</p>
89 <p>Possible values: <em>FormulaBlock | FormulaRows</em>. Default: <em>FormulaBlock</em></p>
90 <p>An example for <em>FormulaBlock</em> output style:</p>
91 <div class="OptionsBox">
92 Formula: H2O
93 <br/> ElementalAnalysis: H: H: 11.1898%; O: 88.8102%
94 <br/> MolecularWeight: 18.0153
95 <br/> ExactMass: 18.0106
96 <br/> ... ...
97 <br/> ... ...
98 <br/> ... ...</div>
99 <div class="OptionsBox">
100 Formula: H2O2
101 <br/> ElementalAnalysis: H: 5.9265%; O: 94.0735%
102 <br/> MolecularWeight: 34.0147
103 <br/> ExactMass: 34.0055
104 <br/> ... ...
105 <br/> ... ...
106 <br/> ... ...</div>
107 <p>An example for <em>FormulaRows</em> output style:</p>
108 <div class="OptionsBox">
109 Formula,ElementalAnalysis,MolecularWeight,ExactMass
110 <br/> H2O,H: 11.1898%; O: 88.8102%,18.0153,18.0106
111 <br/> H2O2,H: 5.9265%; O: 94.0735%,34.0147,34.0055</div>
112 </dd>
113 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
114 <dd>
115 <p>Overwrite existing files.</p>
116 </dd>
117 <dt><strong><strong>--precision</strong> <em>number</em></strong></dt>
118 <dd>
119 <p>Precision for listing numerical values. Default: up to <em>4</em> decimal places.
120 Valid values: positive integers.</p>
121 </dd>
122 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
123 <dd>
124 <p>New text file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. File name is only
125 used during <em>File</em> value of <strong>-o, --output</strong> option.</p>
126 <p>Default file name: FormulsElementalAnalysis.&lt;Ext&gt;. The csv, and tsv
127 &lt;Ext&gt; values are used for comma/semicolon, and tab delimited text files respectively.</p>
128 </dd>
129 <dt><strong><strong>-v --valuelabels</strong> <em>Name,Label,[Name,Label,...]</em></strong></dt>
130 <dd>
131 <p>Specify labels to use for calculated values. In general, it's a comma delimited
132 list of value name and column label pairs. Supported value names: <em>ElementalAnalysis,
133 MolecularWeight, and ExactMass</em>. Default labels: <em>ElementalAnalysis, MolecularWeight,
134 and ExactMass</em>.</p>
135 </dd>
136 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
137 <dd>
138 <p>Location of working directory. Default: current directory.</p>
139 </dd>
140 </dl>
141 <p>
142 </p>
143 <h2>EXAMPLES</h2>
144 <p>To perform elemental analysis, calculate molecular weight and exact mass for H2O,
145 type:</p>
146 <div class="ExampleBox">
147 % ElementalAnalysis.pl</div>
148 <p>To perform elemental analysis, calculate molecular weight and exact mass for
149 Ca3(PO4)2 and [PCl4]+, type:</p>
150 <div class="ExampleBox">
151 % ElementalAnalysis.pl &quot;Ca3(PO4)2&quot; &quot;[PCl4]+&quot;</div>
152 <p>To perform elemental analysis, use label analysis for calculated data, and generate a
153 new CSV file ElementalAnalysis.csv for H2O and H2O2, type:</p>
154 <div class="ExampleBox">
155 % ElementalAnalysis.pl --m ElementalAnalysis --output File
156 --valuelabels &quot;ElementalAnalysis,Analysis&quot; -o -r ElementalAnalysis.csv
157 H2O H2O2</div>
158 <p>To calculate molecular weight and exact mass with four decimal precision and
159 generate a new CSV file WeightAndMass.csv with data rows for H2O and H2O2, type:</p>
160 <div class="ExampleBox">
161 % ElementalAnalysis.pl --m &quot;MolecularWeight,ExactMass&quot; --output File
162 --outputstyle FormulaRows -o -r WeightAndMass.csv
163 H2O H2O2</div>
164 <p>
165 </p>
166 <h2>AUTHOR</h2>
167 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
168 <p>
169 </p>
170 <h2>SEE ALSO</h2>
171 <p><a href="./ElementalAnalysisSDFiles.html">ElementalAnalysisSDFiles.pl</a>,&nbsp<a href="./ElementalAnalysisTextFiles.html">ElementalAnalysisTextFiles.pl</a>
172 </p>
173 <p>
174 </p>
175 <h2>COPYRIGHT</h2>
176 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
177 <p>This file is part of MayaChemTools.</p>
178 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
179 the terms of the GNU Lesser General Public License as published by the Free
180 Software Foundation; either version 3 of the License, or (at your option)
181 any later version.</p>
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