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1
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1 NAME
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2 ElementalAnalysisSDFiles.pl - Perform elemental analysis using formula
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3 data field in SDFile(s)
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4
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5 SYNOPSIS
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6 ElementalAnalysisSDFiles.pl SDFile(s)...
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7
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8 ElementalAnalysisSDFiles.pl [-d, --detail infolevel] [--fast]
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9 [--formulafield SD data field name] [-f, --formulamode *DataField |
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10 StructureData*] [--formulaout yes or no] [-m, --mode All |
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11 "ElementalAnalysis, [MolecularWeight, ExactMass]"] [-h, --help] [-o,
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12 --overwrite] [-r, --root rootname] [-v --valuefieldnames Name, Label,
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13 [Name, Label,...]] [-w, --workingdir dirname] SDFile(s)...
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14
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15 DESCRIPTION
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16 Perform elemental analysis using molecular formula specified by a data
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17 field name or generated from structure data in *SDFile(s)*.
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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 The file names are separated by space.The valid file extensions are
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26 *.sdf* and *.sd*. All other file names are ignored. All the SD files in
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27 a current directory can be specified either by **.sdf* or the current
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28 directory name.
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29
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30 OPTIONS
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31 -d, --detail *infolevel*
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32 Level of information to print about compound records being ignored.
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33 Default: *1*. Possible values: *1, 2 or 3*.
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34
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35 --fast
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36 In this mode, the formula data field specified using -f,
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37 --formulafield option is assumed to contain valid molecular formula
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38 data and initial formula validation check is skipped.
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39
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40 --formulafield *SD data field name*
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41 *SDFile(s)* data field name containing molecular formulas used for
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42 performing elemental analysis during *DataField* value of -f,
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43 --formulamode option. Default value: *SD data field containing the
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44 word formula in its name*.
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45
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46 This option is ignore during *StructureData* value of -f,
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47 --formulamode option.
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48
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49 -f, --formulamode *DataField | StructureData*
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50 Specify source of molecular formula used for performing elemental
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51 analysis: retrieve formula using *SDFile(s)* data field name or
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52 generate formula from structure. Possible values: *DataField or
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53 StructureData*. Default value: *DataField*.
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54
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55 --formulaout *yes or no*
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56 Specify whether to write out formula to SD file during
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57 *StructureData* value of -f, --formulamode option. Possible values:
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58 *Yes or No*. Default: *No*.
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59
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60 -m, --mode *All | "ElementalAnalysis,[MolecularWeight,ExactMass]"*
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61 Specify what values to calculate using molecular formula data field
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62 or structure data from *SDFile(s)*: calculate all supported values
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63 or specify a comma delimited list of values. Possible values: *All |
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64 "ElementalAnalysis, [MolecularWeight, ExactMass]"*. Default: *All*
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65
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66 -h, --help
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67 Print this help message.
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68
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69 -o, --overwrite
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70 Overwrite existing files.
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71
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72 -p, --precision *number*
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73 Precision of calculated values in the output file. Default: up to
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74 *2* decimal places. Valid values: positive integers.
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75
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76 -r, --root *rootname*
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77 New SD file name is generated using the root: <Root>.<Ext>. Default
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78 new file name: <InitialSDFileName>ElementalAnalysis.<Ext>. This
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79 option is ignored for multiple input files.
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80
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81 -v --valuefieldnames *Name,Label,[Name,Label,...]*
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82 Specify SD data field names to use for calculated values. In
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83 general, it's a comma delimited list of value name and SD field name
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84 pairs. Supported value names: *ElementalAnalysis, MolecularWeight,
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85 ExactMass, and MolecularFormula*. Default labels:
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86 *ElementalAnalysis, MolecularWeight, ExactMass, and
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87 MolecularFormula*.
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88
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89 *MolecularFormula* label is only used during *StructureData* value
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90 of -f, --formulamode option.
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91
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92 -w, --workingdir *dirname*
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93 Location of working directory. Default: current directory.
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94
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95 EXAMPLES
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96 To perform elemental analysis, calculate molecular weight and exact mass
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97 using SD field name value with the word Formula in its name and generate
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98 a new SD file NewSample1.sdf, type:
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99
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100 % ElementalAnalysisSDFiles.pl -o -r NewSample1 Sample1.sdf
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101
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102 To perform elemental analysis, calculate molecular weight and exact mass
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103 using structure data in SD file and generate a new SD file
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104 NewSample1.sdf, type:
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105
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106 % ElementalAnalysisSDFiles.pl --formulamode StructureData -o
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107 -r NewSample1 Sample1.sdf
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108
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109 To perform elemental analysis using formulas in SD field name Formula,
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110 use field name Analysis for calculated data, and generate a new SD file
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111 NewSample1.sdf, type:
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112
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113 % ElementalAnalysisSDFiles.pl --m ElementalAnalysis --formulafield
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114 Formula --valuefieldnames "ElementalAnalysis,Analysis" -o
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115 -r NewSample1 Sample1.sdf
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116
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117 To calculate molecular weight, using formulas in SD field name Formula,
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118 with four decimal precision and generate a new SD file NewSample1.sdf,
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119 type
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120
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121 % ElementalAnalysisSDFiles.pl --m MolecularWeight --formulafield
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122 Formula --precision 4 -o -r NewSample1 Sample1.sdf
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123
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124 AUTHOR
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125 Manish Sud <msud@san.rr.com>
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126
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127 SEE ALSO
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128 AnalyzeSDFilesData.pl, InfoSDFiles.pl, ExtractFromSDFiles.pl
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129
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130 COPYRIGHT
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131 Copyright (C) 2015 Manish Sud. All rights reserved.
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132
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133 This file is part of MayaChemTools.
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134
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135 MayaChemTools is free software; you can redistribute it and/or modify it
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136 under the terms of the GNU Lesser General Public License as published by
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137 the Free Software Foundation; either version 3 of the License, or (at
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138 your option) any later version.
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139
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