Mercurial > repos > deepakjadmin > mayatool3_test2
diff docs/scripts/man1/ElementalAnalysis.1 @ 0:4816e4a8ae95 draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/man1/ElementalAnalysis.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,295 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. Capital omega is used to do unbreakable dashes and +.\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, +.\" nothing in troff, for use with C<>. +.tr \(*W- +.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' +.ie n \{\ +. ds -- \(*W- +. ds PI pi +. if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch +. if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch +. ds L" "" +. ds R" "" +. ds C` "" +. ds C' "" +'br\} +.el\{\ +. ds -- \|\(em\| +. ds PI \(*p +. ds L" `` +. ds R" '' +'br\} +.\" +.\" Escape single quotes in literal strings from groff's Unicode transform. +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" +.\" If the F register is turned on, we'll generate index entries on stderr for +.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index +.\" entries marked with X<> in POD. Of course, you'll have to process the +.\" output yourself in some meaningful fashion. +.ie \nF \{\ +. de IX +. tm Index:\\$1\t\\n%\t"\\$2" +.. +. nr % 0 +. rr F +.\} +.el \{\ +. de IX +.. +.\} +.\" +.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2). +.\" Fear. Run. Save yourself. No user-serviceable parts. +. \" fudge factors for nroff and troff +.if n \{\ +. ds #H 0 +. ds #V .8m +. ds #F .3m +. ds #[ \f1 +. ds #] \fP +.\} +.if t \{\ +. ds #H ((1u-(\\\\n(.fu%2u))*.13m) +. ds #V .6m +. ds #F 0 +. ds #[ \& +. ds #] \& +.\} +. \" simple accents for nroff and troff +.if n \{\ +. ds ' \& +. ds ` \& +. ds ^ \& +. ds , \& +. ds ~ ~ +. ds / +.\} +.if t \{\ +. ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u" +. ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u' +. ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u' +. ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u' +. ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u' +. ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u' +.\} +. \" troff and (daisy-wheel) nroff accents +.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V' +.ds 8 \h'\*(#H'\(*b\h'-\*(#H' +.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#] +.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H' +.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u' +.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#] +.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#] +.ds ae a\h'-(\w'a'u*4/10)'e +.ds Ae A\h'-(\w'A'u*4/10)'E +. \" corrections for vroff +.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u' +.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u' +. \" for low resolution devices (crt and lpr) +.if \n(.H>23 .if \n(.V>19 \ +\{\ +. ds : e +. ds 8 ss +. ds o a +. ds d- d\h'-1'\(ga +. ds D- D\h'-1'\(hy +. ds th \o'bp' +. ds Th \o'LP' +. ds ae ae +. ds Ae AE +.\} +.rm #[ #] #H #V #F C +.\" ======================================================================== +.\" +.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 <msud@san.rr.com> +.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.