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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/InfoAminoAcids.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,221 @@ +<html> +<head> +<title>MayaChemTools:Documentation:InfoAminoAcids.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./FilterSDFiles.html" title="FilterSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoFingerprintsFiles.html" title="InfoFingerprintsFiles.html">Next</a></td><td width="34%" align="middle"><strong>InfoAminoAcids.pl</strong></td><td width="33%" align="right"><a href="././code/InfoAminoAcids.html" title="View source code">Code</a> | <a href="./../pdf/InfoAminoAcids.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/InfoAminoAcids.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/InfoAminoAcids.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/InfoAminoAcids.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>InfoAminoAcids.pl - List properties of amino acids</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>InfoAminoAcids.pl AminoAcidIDs...</p> +<p>InfoAminoAcids.pl [<strong>-h, --help</strong>] [<strong>--outdelim</strong> comma | tab | semicolon] +[<strong>--output</strong> STDOUT | File] [<strong>--outputstyle</strong> AminoAcidBlock | AminoAcidRows] +[<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>--propertiesmode</strong> Categories | Names | All] +[<strong>-p, --properties</strong> CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]] +[<strong>--propertieslinting</strong> ByGroup | Alphabetical] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname] +[<strong>-w, --workingdir</strong> dirname] AminoAcidIDs...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>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, DNA and RNA codons, molecular weight - include +variety of other properties: polarity, acidity, hydrophobicity, and so on.</p> +<p> +</p> +<h2>PARAMETERS</h2> +<dl> +<dt><strong><strong>AminoAcidIDs</strong> <em>ThreeLetterCode [OneLetterCode AminoAcidName...]</em></strong></dt> +<dd> +<p><em>AminoAcidIDs</em> is a space delimited list of values to identify amino acids.</p> +<p>Input value format is: <em>ThreeLetterCode [OneLetterCode AminoAcidName...]</em>. Default: <em>Ala</em>. +Examples:</p> +<div class="OptionsBox"> + Ala +<br/> Glu A +<br/> Alanine Glu Y "Aspartic acid"</div> +</dd> +</dl> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt> +<dd> +<p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em> +Default value: <em>comma</em>.</p> +</dd> +<dt><strong><strong>--output</strong> <em>STDOUT | File</em></strong></dt> +<dd> +<p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default: +<em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p> +</dd> +<dt><strong><strong>--outputstyle</strong> <em>AminoAcidBlock | AminoAcidRows</em></strong></dt> +<dd> +<p>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.</p> +<p>Possible values: <em>AminoAcidBlock | AminoAcidRows</em>. Default: <em>AminoAcidBlock</em></p> +<p>An example for <em>AminoAcidBlock</em> output style:</p> +<div class="OptionsBox"> + ThreeLetterCode: Ala +<br/> OneLetterCode: A +<br/> AminoAcid: Alanine +<br/> MolecularWeight: 89.0941 +<br/> ... ... +<br/> ... ... +<br/> ... ...</div> +<div class="OptionsBox"> + ThreeLetterCode: Glu +<br/> OneLetterCode: E +<br/> AminoAcid: Glutamic acid +<br/> MolecularWeight: 147.1308 +<br/> ... ... +<br/> ... ... +<br/> ... ...</div> +<p>An example for <em>AminoAcidRows</em> output style:</p> +<div class="OptionsBox"> + ThreeLetterCode,OneLetterCode,AminoAcid,MolecularWeight +<br/> Ala,A,Alanine,89.0941.. +<br/> Glu,E,Glutamic acid,147.1308..</div> +</dd> +<dt><strong><strong>-o, --overwrite</strong></strong></dt> +<dd> +<p>Overwrite existing files.</p> +</dd> +<dt><strong><strong>--precision</strong> <em>number</em></strong></dt> +<dd> +<p>Precision for listing numerical values. Default: up to <em>4</em> decimal places. +Valid values: positive integers.</p> +</dd> +<dt><strong><strong>--propertiesmode</strong> <em>Categories | Names | All</em></strong></dt> +<dd> +<p>Specify how property names are specified: use category names; explicit list of property names; or +use all available properties. Possible values: <em>Categories, Names, or All</em>. Default: <em>Categories</em>.</p> +<p>This option is used in conjunction with <strong>-p, --properties</strong> option to specify properties of +interest.</p> +</dd> +<dt><strong><strong>-p, --properties</strong> <em>CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]</em></strong></dt> +<dd> +<p>This option is <strong>--propertiesmode</strong> specific. In general, it's a list of comma separated category or +property names.</p> +<p>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.</p> +<p>Possible values: <em>Basic | BasicPlus | BasicAndHydrophobicity | BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]</em>. +Default: <em>Basic</em>.</p> +<p><em>Basic</em> includes: <em>ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4</em></p> +<p><em>BasicPlus</em> includes: <em>ThreeLetterCode, 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</em></p> +<p><em>BasicAndHydrophobicity</em> includes: <em>ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers</em></p> +<p><em>BasicAndHydrophobicityPlus</em> includes: <em>(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</em></p> +<p>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, %AccessibleResidues, %BuriedResidues, 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</p> +</dd> +<dt><strong><strong>--propertieslisting</strong> <em>ByGroup | Alphabetical</em></strong></dt> +<dd> +<p>Specify how to list properties for amino acids: group by category or an alphabetical by +property names. Possible values: <em>ByGroup or Alphabetical</em>. Default: <em>ByGroup</em>.</p> +</dd> +<dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt> +<dd> +<p>Put quotes around column values in output text file. Possible values: <em>yes or +no</em>. Default value: <em>yes</em>.</p> +</dd> +<dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> +<dd> +<p>New text file name is generated using the root: <Root>.<Ext>. File name is only +used during <em>File</em> value of <strong>-o, --output</strong> option.</p> +<p>Default file name: AminoAcidInfo<mode>.<Ext>. The csv, and tsv +<Ext> values are used for comma/semicolon, and tab delimited text files respectively.</p> +</dd> +<dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> +<dd> +<p>Location of working directory. Default: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>To list basic properties information for amino acid Ala, type:</p> +<div class="ExampleBox"> + % InfoAminoAcids.pl</div> +<p>To list all available properties information for amino acid Ala, type:</p> +<div class="ExampleBox"> + % InfoAminoAcids.pl --propertiesmode all</div> +<p>To list basic properties information for amino acids Ala, Arg, and Asp type:</p> +<div class="ExampleBox"> + % InfoAminoAcids.pl Ala Arg Asp + <br/>% InfoAminoAcids.pl A Arg "Aspartic acid"</div> +<p>To list all available properties information for amino acids Ala, Arg, and Asp type:</p> +<div class="ExampleBox"> + % InfoAminoAcids.pl --propertiesmode all Ala Arg Asp</div> +<p>To list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp type:</p> +<div class="ExampleBox"> + % InfoAminoAcids.pl --propertiesmode Categories + --properties BasicAndHydrophobicity Ala Arg Asp</div> +<p>To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight for amino +acids Ala, Arg, and Asp type:</p> +<div class="ExampleBox"> + % InfoAminoAcids.pl --propertiesmode Names + --properties OneLetterCode,ThreeLetterCode,DNACodons,MolecularWeight + Ala Arg Asp</div> +<p>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:</p> +<div class="ExampleBox"> + % InfoAminoAcids.pl --propertiesmode Categories + --properties BasicAndHydrophobicity --propertieslisting alphabetical + --outdelim comma --outputstyle AminoAcidRows --quote yes Ala Arg Asp</div> +<p>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:</p> +<div class="ExampleBox"> + % InfoAminoAcids.pl --propertiesmode Categories + --properties BasicAndHydrophobicity --propertieslisting alphabetical + --outdelim comma --outputstyle AminoAcidRows --quote yes + --output File -r AminoAcidProperties -o Ala Arg Asp</div> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./InfoNucleicAcids.plInfoPeriodicTableElements.html">InfoNucleicAcids.plInfoPeriodicTableElements.pl</a> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>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.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./FilterSDFiles.html" title="FilterSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoFingerprintsFiles.html" title="InfoFingerprintsFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoAminoAcids.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>