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 <msud@san.rr.com>

SEE ALSO
    ElementalAnalysisSDFiles.pl, ElementalAnalysisTextFiles.pl

COPYRIGHT
    Copyright (C) 2015 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.

