comparison mayachemtools/docs/scripts/man1/InfoAminoAcids.1 @ 0:73ae111cf86f draft

Uploaded

0:73ae111cf86f

.\" 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 "INFOAMINOACIDS 1"
.TH INFOAMINOACIDS 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"
InfoAminoAcids.pl \- List properties of amino acids
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
InfoAminoAcids.pl AminoAcidIDs...
.PP
InfoAminoAcids.pl [\fB\-h, \-\-help\fR] [\fB\-\-outdelim\fR comma | tab | semicolon]
[\fB\-\-output\fR \s-1STDOUT\s0 | File] [\fB\-\-outputstyle\fR AminoAcidBlock | AminoAcidRows]
[\fB\-o, \-\-overwrite\fR] [\fB\-\-precision\fR number] [\fB\-\-propertiesmode\fR Categories | Names | All]
[\fB\-p, \-\-properties\fR CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]]
[\fB\-\-propertieslinting\fR ByGroup | Alphabetical] [\fB\-q, \-\-quote\fR yes | no] [\fB\-r, \-\-root\fR rootname]
[\fB\-w, \-\-workingdir\fR dirname] AminoAcidIDs...
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
List amino acid properties. Amino acids identification supports these three types of IDs: one letter
code, three letter code or name. Amino acid properties data, in addition to basic information about
amino acids \- one and three letter codes, name, \s-1DNA\s0 and \s-1RNA\s0 codons, molecular weight \- include
variety of other properties: polarity, acidity, hydrophobicity, and so on.
.SH "PARAMETERS"
.IX Header "PARAMETERS"
.IP "\fBAminoAcidIDs\fR \fIThreeLetterCode [OneLetterCode AminoAcidName...]\fR" 4
.IX Item "AminoAcidIDs ThreeLetterCode [OneLetterCode AminoAcidName...]"
\&\fIAminoAcidIDs\fR is a space delimited list of values to identify amino acids.
.Sp
Input value format is: \fIThreeLetterCode [OneLetterCode AminoAcidName...]\fR. Default: \fIAla\fR.
Examples:
.Sp
.Vb 3
\&    Ala
\&    Glu A
\&    Alanine Glu Y "Aspartic acid"
.Ve
.SH "OPTIONS"
.IX Header "OPTIONS"
.IP "\fB\-h, \-\-help\fR" 4
.IX Item "-h, --help"
Print this help message.
.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 \fIAminoAcidBlock | AminoAcidRows\fR" 4
.IX Item "--outputstyle AminoAcidBlock | AminoAcidRows"
Specify how to list amino acid information: add a new line for each property and present it as a block
for each amino acid; or include all properties in one line and show it as a single line.
.Sp
Possible values: \fIAminoAcidBlock | AminoAcidRows\fR. Default: \fIAminoAcidBlock\fR
.Sp
An example for \fIAminoAcidBlock\fR output style:
.Sp
.Vb 7
\&    ThreeLetterCode: Ala
\&    OneLetterCode: A
\&    AminoAcid: Alanine
\&    MolecularWeight: 89.0941
\&    ... ...
\&    ... ...
\&    ... ...
\&
\&    ThreeLetterCode: Glu
\&    OneLetterCode: E
\&    AminoAcid: Glutamic acid
\&    MolecularWeight: 147.1308
\&    ... ...
\&    ... ...
\&    ... ...
.Ve
.Sp
An example for \fIAminoAcidRows\fR output style:
.Sp
.Vb 3
\&    ThreeLetterCode,OneLetterCode,AminoAcid,MolecularWeight
\&    Ala,A,Alanine,89.0941..
\&    Glu,E,Glutamic acid,147.1308..
.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\-\-propertiesmode\fR \fICategories | Names | All\fR" 4
.IX Item "--propertiesmode Categories | Names | All"
Specify how property names are specified: use category names; explicit list of property names; or
use all available properties. Possible values: \fICategories, Names, or All\fR. Default: \fICategories\fR.
.Sp
This option is used in conjunction with \fB\-p, \-\-properties\fR option to specify properties of
interest.
.IP "\fB\-p, \-\-properties\fR \fICategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]\fR" 4
.IX Item "-p, --properties CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]"
This option is \fB\-\-propertiesmode\fR specific. In general, it's a list of comma separated category or
property names.
.Sp
Specify which amino acid properties information to list for the amino acid IDs specified using command:
line parameters: list basic and/or hydrophobicity information; list all available information; or specify a comma
separated list of amino acid property names.
.Sp
Possible values: \fIBasic | BasicPlus | BasicAndHydrophobicity | BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]\fR.
Default: \fIBasic\fR.
.Sp
\&\fIBasic\fR includes: \fIThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4\fR
.Sp
\&\fIBasicPlus\fR includes: \fIThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), LinearStructure, LinearStructureAtpH7.4\fR
.Sp
\&\fIBasicAndHydrophobicity\fR includes: \fIThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers\fR
.Sp
\&\fIBasicAndHydrophobicityPlus\fR includes: \fI(ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityAbrahamAndLeo, HydrophobicityBlack, HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers, HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers\fR
.Sp
Here is a complete list of available properties: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), vanderWaalsVolume, \f(CW%AccessibleResidues\fR, \f(CW%BuriedResidues\fR, AlphaHelixChouAndFasman, AlphaHelixDeleageAndRoux, AlphaHelixLevitt, AminoAcidsComposition, AminoAcidsCompositionInSwissProt, AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility, BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt, BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt, Bulkiness, CoilDeleageAndRoux, HPLCHFBARetention, HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4, HPLCTFARetention, HydrophobicityAbrahamAndLeo, HydrophobicityBlack, HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers, HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers, ParallelBetaStrand, PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide, RecognitionFactors, Refractivity, RelativeMutability, TotalBetaStrand, LinearStructure, LinearStructureAtpH7.4
.IP "\fB\-\-propertieslisting\fR \fIByGroup | Alphabetical\fR" 4
.IX Item "--propertieslisting ByGroup | Alphabetical"
Specify how to list properties for amino acids: group by category or an alphabetical by
property names. Possible values: \fIByGroup or Alphabetical\fR. Default: \fIByGroup\fR.
.IP "\fB\-q, \-\-quote\fR \fIyes | no\fR" 4
.IX Item "-q, --quote yes | no"
Put quotes around column values in output text file. Possible values: \fIyes or
no\fR. Default value: \fIyes\fR.
.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: AminoAcidInfo<mode>.<Ext>. The csv, and tsv
<Ext> values are used for comma/semicolon, and tab delimited text files respectively.
.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 list basic properties information for amino acid Ala, type:
.PP
.Vb 1
\&    % InfoAminoAcids.pl
.Ve
.PP
To list all available properties information for amino acid Ala, type:
.PP
.Vb 1
\&    % InfoAminoAcids.pl \-\-propertiesmode all
.Ve
.PP
To list basic properties information for amino acids Ala, Arg, and Asp type:
.PP
.Vb 2
\&    % InfoAminoAcids.pl Ala Arg Asp
\&    % InfoAminoAcids.pl A Arg "Aspartic acid"
.Ve
.PP
To list all available properties information for amino acids Ala, Arg, and Asp type:
.PP
.Vb 1
\&    % InfoAminoAcids.pl \-\-propertiesmode all Ala Arg Asp
.Ve
.PP
To list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp type:
.PP
.Vb 2
\&    % InfoAminoAcids.pl \-\-propertiesmode Categories
\&      \-\-properties BasicAndHydrophobicity Ala Arg Asp
.Ve
.PP
To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight for amino
acids Ala, Arg, and Asp type:
.PP
.Vb 3
\&    % InfoAminoAcids.pl \-\-propertiesmode Names
\&      \-\-properties OneLetterCode,ThreeLetterCode,DNACodons,MolecularWeight
\&      Ala Arg Asp
.Ve
.PP
To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp
in rows insetad of amino acid blocks with quotes around the values, type:
.PP
.Vb 3
\&    % InfoAminoAcids.pl \-\-propertiesmode Categories
\&      \-\-properties BasicAndHydrophobicity \-\-propertieslisting alphabetical
\&      \-\-outdelim comma \-\-outputstyle AminoAcidRows \-\-quote yes Ala Arg Asp
.Ve
.PP
To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp
in rows insetad of amino acid blocks with quotes around the values and write them into a file
AminoAcidProperties.csv, type:
.PP
.Vb 4
\&    % InfoAminoAcids.pl \-\-propertiesmode Categories
\&      \-\-properties BasicAndHydrophobicity \-\-propertieslisting alphabetical
\&      \-\-outdelim comma \-\-outputstyle AminoAcidRows \-\-quote yes
\&      \-\-output File \-r AminoAcidProperties \-o Ala Arg Asp
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
InfoNucleicAcids.pl InfoPeriodicTableElements.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.