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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/modules/html/AminoAcids.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,134 @@ +<html> +<head> +<title>MayaChemTools:Documentation:AminoAcids.pm</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="./index.html" title="index.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./Atom.html" title="Atom.html">Next</a></td><td width="34%" align="middle"><strong>AminoAcids.pm</strong></td><td width="33%" align="right"><a href="././code/AminoAcids.html" title="View source code">Code</a> | <a href="./../pdf/AminoAcids.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/AminoAcids.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/AminoAcids.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/AminoAcids.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>AminoAcids</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use AminoAcids;</p> +<p>use AminoAcids qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>AminoAcids</strong> module provides the following functions:</p> +<p> <a href="#getaminoacidpropertiesdata">GetAminoAcidPropertiesData</a>, <a href="#getaminoacidpropertiesnames">GetAminoAcidPropertiesNames</a>, GetAminoAcid<PropertyName> +, <a href="#getaminoacids">GetAminoAcids</a>, <a href="#isaminoacid">IsAminoAcid</a>, <a href="#isaminoacidproperty">IsAminoAcidProperty</a> +</p><p> +</p> +<h2>FUNCTIONS</h2> +<dl> +<dt><strong><a name="getaminoacidpropertiesdata" class="item"><strong>GetAminoAcidPropertiesData</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $DataHashRef = GetAminoAcidPropertiesData($AminoAcidID);</div> +<p>Returns a reference to hash containing property names and values for a specified +amino acid.</p> +</dd> +<dt><strong><a name="getaminoacidpropertiesnames" class="item"><strong>GetAminoAcidPropertiesNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Names = GetAminoAcidPropertiesNames([$Mode]); +<br/> $NamesRef = GetAminoAcidPropertiesNames([$Mode]);</div> +<p>Returns an array or a reference to an array containing names of amino acids +properties. Order of amino acids properties is controlled by optional parameter +<em>Mode</em>. Possible values for <em>Mode</em>: <em>Alphabetical or ByGroup</em>; Default: <em>ByGroup</em></p> +</dd> +<dt><strong><a name="getaminoacidpropertyname" class="item"><strong>GetAminoAcidPropertyName</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Value = GetAminoAcid<PropertyName>($AminoAcidID);</div> +<p>Returns amino acid property value for a specified amino acid. These functions are +not defined in this modules; these are implemented on the fly using Perl's AUTOLOAD +funcion. Here is the list of known amino acids <em>property names</em>: 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><a name="getaminoacids" class="item"><strong>GetAminoAcids</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NamesRef = GetAminoAcids([$NameType]); +<br/> (@Names) = GetAminoAcids([$NameType]);</div> +<p>Returns an array or a reference to an array containing names of amino acids +as one letter code, three letter code, or amino acid name controlled by optional +parameter $NameType. By default, amino acids names are returned as three +letter code. Possible values for <em>NameType</em>: <em>ThreeLetterCode, OneLetterCode, or +AminoAcid</em>.</p> +</dd> +<dt><strong><a name="isaminoacid" class="item"><strong>IsAminoAcid</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = IsAminoAcid($AminoAcidID);</div> +<p>Returns a flag indicating whether or not its a known amino acid ID.</p> +</dd> +<dt><strong><a name="isaminoacidproperty" class="item"><strong>IsAminoAcidProperty</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = IsAminoAcid($PropertyName);</div> +<p>Returns a flag indicating whether or not its a known amino acid property name.</p> +</dd> +</dl> +<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="./NucleicAcids.html">NucleicAcids.pm</a>, <a href="./PeriodicTable.html">PeriodicTable.pm</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="./index.html" title="index.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./Atom.html" title="Atom.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>AminoAcids.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>