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NAME - Perform elemental analysis using formula column in TextFile(s)

SYNOPSIS TextFile(s)... [-c, --colmode colnum | collabel] [-d, --detail infolevel] [-f, --fast] [-f, --formulacol colnum | collabel] [-h, --help] [--indelim comma | semicolon] [-m, --mode All | "ElementalAnysis, [MolecularWeight, ExactMass]"] [-o, --overwrite] [--outdelim comma | tab | semicolon] [-p, --precision number] [-q, --quote yes | no] [-r, --root rootname] [-s, --startcol colnum | collabel] [--startcolmode before | after] -v --valuecollabels [Name, Label, [Name, Label,...]] [-w, --workingdir dirname] TextFile(s)...


Perform elemental analysis using molecular formula column specified by a column number or label in TextFile(s).

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.

The valid file extensions are .csv and .tsv for comma/semicolon and tab delimited text files respectively. All other file names are ignored. All the text files in a current directory can be specified by *.csv, *.tsv, or the current directory name. The --indelim option determines the format of TextFile(s). Any file which doesn't correspond to the format indicated by --indelim option is ignored.


-c, --colmode colnum | collabel

Specify how columns are identified in TextFile(s): using column number or column label. Possible values: colnum or collabel. Default value: colnum.

-d, --detail infolevel

Level of information to print about lines being ignored. Default: 1. Possible values: 1, 2 or 3.

-h, --help

Print this help message.


In this mode, the formula column specified using -f, --formulacol option is assumed to contain valid molecular formula data and initial formula validation check is skipped.

-f, --formulacol col number | col name

This value is mode specific. It specifies molecular formula column to use for performing elemental analysis on TextFile(s). Possible values: col number or col label. Default value: first column containing the word formula in its column label.

-m, --mode All | "ElementalAnalysis,[MolecularWeight,ExactMass]"

Specify what values to calculate using molecular formula in TextFile(s): calculate all supported values or specify a comma delimited list of values. Possible values: All | "ElementalAnalysis, [MolecularWeight, ExactMass]". Default: All

--indelim comma | semicolon

Input delimiter for CSV TextFile(s). Possible values: comma or semicolon. Default value: comma. For TSV files, this option is ignored and tab is used as a delimiter.

-o, --overwrite

Overwrite existing files.

--outdelim comma | tab | semicolon

Output text file delimiter. Possible values: comma, tab, or semicolon Default value: comma.

-p, --precision number

Precision of calculated values in the output file. Default: up to 2 decimal places. Valid values: positive integers.

-q, --quote yes | no

Put quotes around column values in output text file. Possible values: yes or no. Default value: yes.

-r, --root rootname

New text file name is generated using the root: <Root>.<Ext>. Default new file name: <InitialTextFileName>ElementalAnalysis.<Ext>. The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text files respectively. This option is ignored for multiple input files.

-s, --startcol colnum | collabel

This value is mode specific. It specifies the column in text files which is used for start adding calculated column values. For colnum mode, specify column number and for collabel mode, specify column label.

Default value: last. Start merge after the last column.

--startcolmode before | after

Start adding calculated column values after the -s, --startcol value. Possible values: before or after. Default value: after.

-v --valuecollabels Name,Label,[Name,Label,...]

Specify column 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.


To perform elemental analysis, calculate molecular weight and exact mass using formulas in a column with the word Formula in its column label and generate a new CSV text file NewSample1.csv, type:

% -o -r NewSample1 Sample1.csv

To perform elemental analysis using formulas in column number two, use column label Analysis for calculated data, and generate a new CSV text file NewSample1.csv, type:

% --m ElementalAnalysis --formulacol 2 --valuecollabels "ElementalAnalysis,Analysis" -o -r NewSample1 Sample1.csv

To calculate molecular weight using formula in column label Formula with four decimal precision and generate a new CSV text file NewSample1.csv, type

% --m MolecularWeight --colmode collabel --formulacol Formula --precision 4 -o -r NewSample1 Sample1.csv

To calculate exact mass using formula in column label Formula with four decimal precision, adding column for exact mass right after Formula column, and generate a new CSV text file NewSample1.csv, type

% --m ExactMass --colmode collabel --formulacol Formula --precision 4 --startcolmode after --startcol Formula -o -r NewSample1 Sample1.csv


Manish Sud



Copyright (C) 2013 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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