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