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diff mayachemtools/docs/scripts/man1/InfoAminoAcids.1 @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/man1/InfoAminoAcids.1 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,341 @@ +.\" 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++. 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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 <msud@san.rr.com> +.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.