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1 NAME
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2 ElementalAnalysis.pl - Perform elemental analysis using specified
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3 formulas
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4
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5 SYNOPSIS
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6 ElementalAnalysis.pl Formula(s)...
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7
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8 ElementalAnalysis.pl [-h, --help] [-m, --mode All | "ElementalAnalysis,
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9 [MolecularWeight, ExactMass]"] [--outdelim comma | tab | semicolon]
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10 [--output STDOUT | File] [--outputstyle FormulaBlock | FormulaRows] [-o,
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11 --overwrite] [--precision number] [-q, --quote yes | no] [-r, --root
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12 rootname] [-v --valuelabels [Name, Label, [Name, Label,...]] [-w,
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13 --workingdir dirname] Formula(s)...
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14
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15 DESCRIPTION
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16 Perform elemental analysis using molecular formula(s) specified on the
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17 command line.
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18
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19 In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
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20 other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-,
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21 C37H42N2O6+2, Na2CO3.10H2O, 8H2S.46H2O, and so on. Charges are simply
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22 ignored. Isotope symbols in formulas specification, including D and T,
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23 are not supported.
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24
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25 PARAMETERS
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26 Formulas *Formula1 [Formula2...]*
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27 *Formulas* is a space delimited list of molecular formulas to use
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28 for elemental analysis.
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29
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30 Input value format is: *Formula1 [Formula2 Formula3...]*. Default:
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31 *H2O*. Examples:
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32
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33 HCl
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34 HCl, C3H7O2N
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35 H2O2 Ca3(PO4)2 [PCl4]+
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36
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37 OPTIONS
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38 -h, --help
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39 Print this help message.
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40
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41 --fast
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42 In this mode, the specified formulas are considered valid and
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43 initial formula validation check is skipped.
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44
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45 -m, --mode *All | "ElementalAnalysis,[MolecularWeight,ExactMass]"*
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46 Specify what values to calculate using molecular formulas specified
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47 on command line: calculate all supported values or specify a comma
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48 delimited list of values. Possible values: *All |
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49 "ElementalAnalysis, [MolecularWeight, ExactMass]"*. Default: *All*.
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50
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51 --outdelim *comma | tab | semicolon*
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52 Output text file delimiter. Possible values: *comma, tab, or
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53 semicolon* Default value: *comma*.
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54
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55 --output *STDOUT | File*
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56 List information at STDOUT or write it to a file. Possible values:
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57 *STDOUT or File*. Default: *STDOUT*. -r, --root option is used to
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58 generate output file name.
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59
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60 --outputstyle *FormulaBlock | FormulaRows*
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61 Specify how to list calculated values: add a new line for each
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62 property and present it as a block for each formula; or include all
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63 properties in one line and show it as a single line.
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64
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65 Possible values: *FormulaBlock | FormulaRows*. Default:
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66 *FormulaBlock*
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67
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68 An example for *FormulaBlock* output style:
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69
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70 Formula: H2O
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71 ElementalAnalysis: H: H: 11.1898%; O: 88.8102%
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72 MolecularWeight: 18.0153
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73 ExactMass: 18.0106
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74 ... ...
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75 ... ...
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76 ... ...
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77
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78 Formula: H2O2
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79 ElementalAnalysis: H: 5.9265%; O: 94.0735%
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80 MolecularWeight: 34.0147
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81 ExactMass: 34.0055
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82 ... ...
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83 ... ...
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84 ... ...
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85
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86 An example for *FormulaRows* output style:
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87
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88 Formula,ElementalAnalysis,MolecularWeight,ExactMass
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89 H2O,H: 11.1898%; O: 88.8102%,18.0153,18.0106
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90 H2O2,H: 5.9265%; O: 94.0735%,34.0147,34.0055
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91
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92 -o, --overwrite
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93 Overwrite existing files.
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94
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95 --precision *number*
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96 Precision for listing numerical values. Default: up to *4* decimal
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97 places. Valid values: positive integers.
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98
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99 -r, --root *rootname*
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100 New text file name is generated using the root: <Root>.<Ext>. File
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101 name is only used during *File* value of -o, --output option.
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102
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103 Default file name: FormulsElementalAnalysis.<Ext>. The csv, and tsv
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104 <Ext> values are used for comma/semicolon, and tab delimited text
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105 files respectively.
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106
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107 -v --valuelabels *Name,Label,[Name,Label,...]*
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108 Specify labels to use for calculated values. In general, it's a
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109 comma delimited list of value name and column label pairs. Supported
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110 value names: *ElementalAnalysis, MolecularWeight, and ExactMass*.
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111 Default labels: *ElementalAnalysis, MolecularWeight, and ExactMass*.
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112
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113 -w, --workingdir *dirname*
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114 Location of working directory. Default: current directory.
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115
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116 EXAMPLES
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117 To perform elemental analysis, calculate molecular weight and exact mass
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118 for H2O, type:
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119
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120 % ElementalAnalysis.pl
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121
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122 To perform elemental analysis, calculate molecular weight and exact mass
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123 for Ca3(PO4)2 and [PCl4]+, type:
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124
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125 % ElementalAnalysis.pl "Ca3(PO4)2" "[PCl4]+"
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126
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127 To perform elemental analysis, use label analysis for calculated data,
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128 and generate a new CSV file ElementalAnalysis.csv for H2O and H2O2,
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129 type:
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130
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131 % ElementalAnalysis.pl --m ElementalAnalysis --output File
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132 --valuelabels "ElementalAnalysis,Analysis" -o -r ElementalAnalysis.csv
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133 H2O H2O2
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134
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135 To calculate molecular weight and exact mass with four decimal precision
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136 and generate a new CSV file WeightAndMass.csv with data rows for H2O and
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137 H2O2, type:
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138
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139 % ElementalAnalysis.pl --m "MolecularWeight,ExactMass" --output File
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140 --outputstyle FormulaRows -o -r WeightAndMass.csv
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141 H2O H2O2
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142
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143 AUTHOR
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144 Manish Sud <msud@san.rr.com>
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145
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146 SEE ALSO
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147 ElementalAnalysisSDFiles.pl, ElementalAnalysisTextFiles.pl
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148
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149 COPYRIGHT
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150 Copyright (C) 2015 Manish Sud. All rights reserved.
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151
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152 This file is part of MayaChemTools.
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153
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154 MayaChemTools is free software; you can redistribute it and/or modify it
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155 under the terms of the GNU Lesser General Public License as published by
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156 the Free Software Foundation; either version 3 of the License, or (at
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157 your option) any later version.
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158
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