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3 <title>MayaChemTools:Documentation:ElementalAnalysis.pl</title>
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11 </center>
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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="./DBTablesToTextFiles.html" title="DBTablesToTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/ElementalAnalysis.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ElementalAnalysis.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ElementalAnalysis.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ElementalAnalysis.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>ElementalAnalysis.pl - Perform elemental analysis using specified formulas</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>ElementalAnalysis.pl Formula(s)...</p>
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26 <p>ElementalAnalysis.pl [<strong>-h, --help</strong>]
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27 [<strong>-m, --mode</strong> All | "ElementalAnalysis, [MolecularWeight, ExactMass]"]
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28 [<strong>--outdelim</strong> comma | tab | semicolon]
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29 [<strong>--output</strong> STDOUT | File] [<strong>--outputstyle</strong> FormulaBlock | FormulaRows]
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30 [<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname]
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31 [<strong>-v --valuelabels</strong> [Name, Label, [Name, Label,...]]
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32 [<strong>-w, --workingdir</strong> dirname] Formula(s)...</p>
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33 <p>
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34 </p>
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35 <h2>DESCRIPTION</h2>
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36 <p>Perform elemental analysis using molecular formula(s) specified on the command line.</p>
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37 <p>In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
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38 other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O,
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39 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
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40 D and T, are not supported.</p>
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41 <p>
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42 </p>
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43 <h2>PARAMETERS</h2>
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44 <dl>
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45 <dt><strong><strong>Formulas</strong> <em>Formula1 [Formula2...]</em></strong></dt>
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46 <dd>
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47 <p><em>Formulas</em> is a space delimited list of molecular formulas to use for elemental analysis.</p>
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48 <p>Input value format is: <em>Formula1 [Formula2 Formula3...]</em>. Default: <em>H2O</em>.
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49 Examples:</p>
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50 <div class="OptionsBox">
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51 HCl
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52 <br/> HCl, C3H7O2N
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53 <br/> H2O2 Ca3(PO4)2 [PCl4]+</div>
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54 </dd>
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55 </dl>
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56 <p>
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57 </p>
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58 <h2>OPTIONS</h2>
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59 <dl>
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60 <dt><strong><strong>-h, --help</strong></strong></dt>
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61 <dd>
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62 <p>Print this help message.</p>
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63 </dd>
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64 <dt><strong><strong>--fast</strong></strong></dt>
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65 <dd>
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66 <p>In this mode, the specified formulas are considered valid and initial formula
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67 validation check is skipped.</p>
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68 </dd>
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69 <dt><strong><strong>-m, --mode</strong> <em>All | "ElementalAnalysis,[MolecularWeight,ExactMass]"</em></strong></dt>
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70 <dd>
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71 <p>Specify what values to calculate using molecular formulas specified on command
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72 line: calculate all supported values or specify a comma delimited list of values. Possible
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73 values: <em>All | "ElementalAnalysis, [MolecularWeight, ExactMass]"</em>. Default: <em>All</em>.</p>
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74 </dd>
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75 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt>
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76 <dd>
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77 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>
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78 Default value: <em>comma</em>.</p>
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79 </dd>
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80 <dt><strong><strong>--output</strong> <em>STDOUT | File</em></strong></dt>
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81 <dd>
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82 <p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default:
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83 <em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p>
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84 </dd>
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85 <dt><strong><strong>--outputstyle</strong> <em>FormulaBlock | FormulaRows</em></strong></dt>
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86 <dd>
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87 <p>Specify how to list calculated values: add a new line for each property and present it as a block
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88 for each formula; or include all properties in one line and show it as a single line.</p>
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89 <p>Possible values: <em>FormulaBlock | FormulaRows</em>. Default: <em>FormulaBlock</em></p>
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90 <p>An example for <em>FormulaBlock</em> output style:</p>
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91 <div class="OptionsBox">
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92 Formula: H2O
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93 <br/> ElementalAnalysis: H: H: 11.1898%; O: 88.8102%
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94 <br/> MolecularWeight: 18.0153
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95 <br/> ExactMass: 18.0106
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96 <br/> ... ...
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97 <br/> ... ...
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98 <br/> ... ...</div>
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99 <div class="OptionsBox">
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100 Formula: H2O2
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101 <br/> ElementalAnalysis: H: 5.9265%; O: 94.0735%
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102 <br/> MolecularWeight: 34.0147
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103 <br/> ExactMass: 34.0055
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104 <br/> ... ...
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105 <br/> ... ...
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106 <br/> ... ...</div>
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107 <p>An example for <em>FormulaRows</em> output style:</p>
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108 <div class="OptionsBox">
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109 Formula,ElementalAnalysis,MolecularWeight,ExactMass
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110 <br/> H2O,H: 11.1898%; O: 88.8102%,18.0153,18.0106
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111 <br/> H2O2,H: 5.9265%; O: 94.0735%,34.0147,34.0055</div>
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112 </dd>
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113 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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114 <dd>
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115 <p>Overwrite existing files.</p>
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116 </dd>
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117 <dt><strong><strong>--precision</strong> <em>number</em></strong></dt>
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118 <dd>
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119 <p>Precision for listing numerical values. Default: up to <em>4</em> decimal places.
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120 Valid values: positive integers.</p>
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121 </dd>
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122 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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123 <dd>
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124 <p>New text file name is generated using the root: <Root>.<Ext>. File name is only
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125 used during <em>File</em> value of <strong>-o, --output</strong> option.</p>
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126 <p>Default file name: FormulsElementalAnalysis.<Ext>. The csv, and tsv
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127 <Ext> values are used for comma/semicolon, and tab delimited text files respectively.</p>
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128 </dd>
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129 <dt><strong><strong>-v --valuelabels</strong> <em>Name,Label,[Name,Label,...]</em></strong></dt>
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130 <dd>
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131 <p>Specify labels to use for calculated values. In general, it's a comma delimited
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132 list of value name and column label pairs. Supported value names: <em>ElementalAnalysis,
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133 MolecularWeight, and ExactMass</em>. Default labels: <em>ElementalAnalysis, MolecularWeight,
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134 and ExactMass</em>.</p>
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135 </dd>
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136 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
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137 <dd>
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138 <p>Location of working directory. Default: current directory.</p>
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139 </dd>
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140 </dl>
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141 <p>
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142 </p>
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143 <h2>EXAMPLES</h2>
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144 <p>To perform elemental analysis, calculate molecular weight and exact mass for H2O,
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145 type:</p>
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146 <div class="ExampleBox">
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147 % ElementalAnalysis.pl</div>
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148 <p>To perform elemental analysis, calculate molecular weight and exact mass for
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149 Ca3(PO4)2 and [PCl4]+, type:</p>
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150 <div class="ExampleBox">
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151 % ElementalAnalysis.pl "Ca3(PO4)2" "[PCl4]+"</div>
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152 <p>To perform elemental analysis, use label analysis for calculated data, and generate a
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153 new CSV file ElementalAnalysis.csv for H2O and H2O2, type:</p>
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154 <div class="ExampleBox">
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155 % ElementalAnalysis.pl --m ElementalAnalysis --output File
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156 --valuelabels "ElementalAnalysis,Analysis" -o -r ElementalAnalysis.csv
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157 H2O H2O2</div>
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158 <p>To calculate molecular weight and exact mass with four decimal precision and
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159 generate a new CSV file WeightAndMass.csv with data rows for H2O and H2O2, type:</p>
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160 <div class="ExampleBox">
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161 % ElementalAnalysis.pl --m "MolecularWeight,ExactMass" --output File
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162 --outputstyle FormulaRows -o -r WeightAndMass.csv
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163 H2O H2O2</div>
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164 <p>
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165 </p>
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166 <h2>AUTHOR</h2>
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167 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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168 <p>
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169 </p>
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170 <h2>SEE ALSO</h2>
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171 <p><a href="./ElementalAnalysisSDFiles.html">ElementalAnalysisSDFiles.pl</a>, <a href="./ElementalAnalysisTextFiles.html">ElementalAnalysisTextFiles.pl</a>
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172 </p>
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173 <p>
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174 </p>
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175 <h2>COPYRIGHT</h2>
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176 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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177 <p>This file is part of MayaChemTools.</p>
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178 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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179 the terms of the GNU Lesser General Public License as published by the Free
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180 Software Foundation; either version 3 of the License, or (at your option)
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181 any later version.</p>
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182 <p> </p><p> </p><div class="DocNav">
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183 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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184 <tr align="left" valign="top"><td width="33%" align="left"><a href="./DBTablesToTextFiles.html" title="DBTablesToTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ElementalAnalysisSDFiles.html" title="ElementalAnalysisSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ElementalAnalysis.pl</strong></td></tr>
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185 </table>
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186 </div>
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187 <br />
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188 <center>
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189 <img src="../../images/h2o2.png">
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190 </center>
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192 </html>
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