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# 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) 2018 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.

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