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.\" ========================================================================
.\"
.IX Title "ELEMENTALANALYSIS 1"
.TH ELEMENTALANALYSIS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
ElementalAnalysis.pl \- Perform elemental analysis using specified formulas
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
ElementalAnalysis.pl Formula(s)...
.PP
ElementalAnalysis.pl [\fB\-h, \-\-help\fR]
[\fB\-m, \-\-mode\fR All | \*(L"ElementalAnalysis, [MolecularWeight, ExactMass]\*(R"]
[\fB\-\-outdelim\fR comma | tab | semicolon]
[\fB\-\-output\fR \s-1STDOUT\s0 | File] [\fB\-\-outputstyle\fR FormulaBlock | FormulaRows]
[\fB\-o, \-\-overwrite\fR] [\fB\-\-precision\fR number] [\fB\-q, \-\-quote\fR yes | no] [\fB\-r, \-\-root\fR rootname]
[\fB\-v \-\-valuelabels\fR [Name, Label, [Name, Label,...]]
[\fB\-w, \-\-workingdir\fR dirname] Formula(s)...
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Perform elemental analysis using molecular formula(s) specified on the command line.
.PP
In addition to straightforward molecular formulas \- H2O, HCl, C3H7O2N \-
other supported variations are: Ca3(\s-1PO4\s0)2, [PCl4]+, [Fe(\s-1CN\s0)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.
.SH "PARAMETERS"
.IX Header "PARAMETERS"
.IP "\fBFormulas\fR \fIFormula1 [Formula2...]\fR" 4
.IX Item "Formulas Formula1 [Formula2...]"
\&\fIFormulas\fR is a space delimited list of molecular formulas to use for elemental analysis.
.Sp
Input value format is: \fIFormula1 [Formula2 Formula3...]\fR. Default: \fIH2O\fR.
Examples:
.Sp
.Vb 3
\&    HCl
\&    HCl, C3H7O2N
\&    H2O2 Ca3(PO4)2 [PCl4]+
.Ve
.SH "OPTIONS"
.IX Header "OPTIONS"
.IP "\fB\-h, \-\-help\fR" 4
.IX Item "-h, --help"
Print this help message.
.IP "\fB\-\-fast\fR" 4
.IX Item "--fast"
In this mode, the specified formulas are considered valid and initial formula
validation check is skipped.
.ie n .IP "\fB\-m, \-\-mode\fR \fIAll | ""ElementalAnalysis,[MolecularWeight,ExactMass]""\fR" 4
.el .IP "\fB\-m, \-\-mode\fR \fIAll | ``ElementalAnalysis,[MolecularWeight,ExactMass]''\fR" 4
.IX Item "-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: \fIAll | \*(L"ElementalAnalysis, [MolecularWeight, ExactMass]\*(R"\fR. Default: \fIAll\fR.
.IP "\fB\-\-outdelim\fR \fIcomma | tab | semicolon\fR" 4
.IX Item "--outdelim comma | tab | semicolon"
Output text file delimiter. Possible values: \fIcomma, tab, or semicolon\fR
Default value: \fIcomma\fR.
.IP "\fB\-\-output\fR \fI\s-1STDOUT\s0 | File\fR" 4
.IX Item "--output STDOUT | File"
List information at \s-1STDOUT\s0 or write it to a file. Possible values: \fI\s-1STDOUT\s0 or File\fR. Default:
\&\fI\s-1STDOUT\s0\fR. \fB\-r, \-\-root\fR option is used to generate output file name.
.IP "\fB\-\-outputstyle\fR \fIFormulaBlock | FormulaRows\fR" 4
.IX Item "--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.
.Sp
Possible values: \fIFormulaBlock | FormulaRows\fR. Default: \fIFormulaBlock\fR
.Sp
An example for \fIFormulaBlock\fR output style:
.Sp
.Vb 7
\&    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
\&    ... ...
\&    ... ...
\&    ... ...
.Ve
.Sp
An example for \fIFormulaRows\fR output style:
.Sp
.Vb 3
\&    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
.Ve
.IP "\fB\-o, \-\-overwrite\fR" 4
.IX Item "-o, --overwrite"
Overwrite existing files.
.IP "\fB\-\-precision\fR \fInumber\fR" 4
.IX Item "--precision number"
Precision for listing numerical values. Default: up to \fI4\fR decimal places.
Valid values: positive integers.
.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
.IX Item "-r, --root rootname"
New text file name is generated using the root: <Root>.<Ext>. File name is only
used during \fIFile\fR value of \fB\-o, \-\-output\fR option.
.Sp
Default file name: FormulsElementalAnalysis.<Ext>. The csv, and tsv
<Ext> values are used for comma/semicolon, and tab delimited text files respectively.
.IP "\fB\-v \-\-valuelabels\fR \fIName,Label,[Name,Label,...]\fR" 4
.IX Item "-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: \fIElementalAnalysis,
MolecularWeight,  and ExactMass\fR. Default labels: \fIElementalAnalysis, MolecularWeight,
and ExactMass\fR.
.IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4
.IX Item "-w, --workingdir dirname"
Location of working directory. Default: current directory.
.SH "EXAMPLES"
.IX Header "EXAMPLES"
To perform elemental analysis, calculate molecular weight and exact mass for H2O,
type:
.PP
.Vb 1
\&    % ElementalAnalysis.pl
.Ve
.PP
To perform elemental analysis, calculate molecular weight and exact mass for
Ca3(\s-1PO4\s0)2 and [PCl4]+, type:
.PP
.Vb 1
\&    % ElementalAnalysis.pl "Ca3(PO4)2" "[PCl4]+"
.Ve
.PP
To perform elemental analysis, use label analysis for calculated data, and generate a
new \s-1CSV\s0 file ElementalAnalysis.csv for H2O and H2O2, type:
.PP
.Vb 3
\&    % ElementalAnalysis.pl \-\-m ElementalAnalysis \-\-output File
\&      \-\-valuelabels "ElementalAnalysis,Analysis" \-o \-r ElementalAnalysis.csv
\&      H2O H2O2
.Ve
.PP
To calculate molecular weight and exact mass with four decimal precision and
generate a new \s-1CSV\s0 file WeightAndMass.csv with data rows for H2O and H2O2, type:
.PP
.Vb 3
\&    % ElementalAnalysis.pl \-\-m "MolecularWeight,ExactMass" \-\-output File
\&      \-\-outputstyle FormulaRows \-o \-r WeightAndMass.csv
\&      H2O H2O2
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
ElementalAnalysisSDFiles.pl, ElementalAnalysisTextFiles.pl
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
Copyright (C) 2015 Manish Sud. All rights reserved.
.PP
This file is part of MayaChemTools.
.PP
MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.