NAME
ElementalAnalysis.pl - Perform elemental analysis using specified formulas
SYNOPSIS
ElementalAnalysis.pl Formula(s)...
ElementalAnalysis.pl [-h, --help]
[-m, --mode All | ''ElementalAnalysis, [MolecularWeight, ExactMass]'']
[--outdelim comma | tab | semicolon]
[--output STDOUT | File] [--outputstyle FormulaBlock | FormulaRows]
[-o, --overwrite] [--precision number] [-q, --quote yes | no] [-r, --root rootname]
[-v --valuelabels [Name, Label, [Name, Label,...]]
[-w, --workingdir dirname] Formula(s)...
DESCRIPTION
Perform elemental analysis using molecular formula(s) specified on the command line.
In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O,
8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
D and T, are not supported.
PARAMETERS
- Formulas Formula1 [Formula2...]
-
Formulas is a space delimited list of molecular formulas to use for elemental analysis.
-
Input value format is: Formula1 [Formula2 Formula3...]. Default: H2O.
Examples:
-
HCl
HCl, C3H7O2N
H2O2 Ca3(PO4)2 [PCl4]+
OPTIONS
- -h, --help
-
Print this help message
- --fast
-
In this mode, the specified formulas are considered valid and initial formula
validation check is skipped.
- -m, --mode All | ''ElementalAnalysis,[MolecularWeight,ExactMass]''
-
Specify what values to calculate using molecular formulas specified on command
line: calculate all supported values or specify a comma delimited list of values. Possible
values: All | ''ElementalAnalysis, [MolecularWeight, ExactMass]''. Default: All
- --outdelim comma | tab | semicolon
-
Output text file delimiter. Possible values: comma, tab, or semicolon
Default value: comma
- --output STDOUT | File
-
List information at STDOUT or write it to a file. Possible values: STDOUT or File. Default:
STDOUT. -r, --root option is used to generate output file name.
- --outputstyle FormulaBlock | FormulaRows
-
Specify how to list calculated values: add a new line for each property and present it as a block
for each formula; or include all properties in one line and show it as a single line.
-
Possible values: FormulaBlock | FormulaRows. Default: FormulaBlock
-
An example for FormulaBlock output style:
-
Formula: H2O
ElementalAnalysis: H: H: 11.1898%; O: 88.8102%
MolecularWeight: 18.0153
ExactMass: 18.0106
... ...
... ...
... ...
-
Formula: H2O2
ElementalAnalysis: H: 5.9265%; O: 94.0735%
MolecularWeight: 34.0147
ExactMass: 34.0055
... ...
... ...
... ...
-
An example for FormulaRows output style:
-
Formula,ElementalAnalysis,MolecularWeight,ExactMass
H2O,H: 11.1898%; O: 88.8102%,18.0153,18.0106
H2O2,H: 5.9265%; O: 94.0735%,34.0147,34.0055
- -o, --overwrite
-
Overwrite existing files
- --precision number
-
Precision for listing numerical values. Default: up to 4 decimal places.
Valid values: positive integers.
- -r, --root rootname
-
New text file name is generated using the root: <Root>.<Ext>. File name is only
used during File value of -o, --output option.
-
Default file name: FormulsElementalAnalysis.<Ext>. The csv, and tsv
<Ext> values are used for comma/semicolon, and tab delimited text files respectively.
- -v --valuelabels Name,Label,[Name,Label,...]
-
Specify labels to use for calculated values. In general, it's a comma delimited
list of value name and column label pairs. Supported value names: ElementalAnalysis,
MolecularWeight, and ExactMass. Default labels: ElementalAnalysis, MolecularWeight,
and ExactMass.
- -w, --workingdir dirname
-
Location of working directory. Default: current directory
EXAMPLES
To perform elemental analysis, calculate molecular weight and exact mass for H2O,
type:
% ElementalAnalysis.pl
To perform elemental analysis, calculate molecular weight and exact mass for
Ca3(PO4)2 and [PCl4]+, type:
% ElementalAnalysis.pl "Ca3(PO4)2" "[PCl4]+"
To perform elemental analysis, use label analysis for calculated data, and generate a
new CSV file ElementalAnalysis.csv for H2O and H2O2, type:
% ElementalAnalysis.pl --m ElementalAnalysis --output File
--valuelabels "ElementalAnalysis,Analysis" -o -r ElementalAnalysis.csv
H2O H2O2
To calculate molecular weight and exact mass with four decimal precision and
generate a new CSV file WeightAndMass.csv with data rows for H2O and H2O2, type:
% ElementalAnalysis.pl --m "MolecularWeight,ExactMass" --output File
--outputstyle FormulaRows -o -r WeightAndMass.csv
H2O H2O2
AUTHOR
Manish Sud
SEE ALSO
ElementalAnalysisSDFiles.pl, ElementalAnalysisTextFiles.pl
COPYRIGHT
Copyright (C) 2004-2008 Manish Sud. All rights reserved.
This file is part of MayaChemTools.
MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.
