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<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&lt;PropertyName&gt;
, <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">
    $Value = GetAminoAcid&lt;PropertyName&gt;($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>,&nbsp<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>
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