NAME
    AminoAcids

SYNOPSIS
    use AminoAcids;

    use AminoAcids qw(:all);

DESCRIPTION
    AminoAcids module provides the following functions:

    GetAminoAcidPropertiesData, GetAminoAcidPropertiesNames,
    GetAminoAcid<PropertyName>, GetAminoAcids, IsAminoAcid,
    IsAminoAcidProperty

FUNCTIONS
    GetAminoAcidPropertiesData
            $DataHashRef = GetAminoAcidPropertiesData($AminoAcidID);

        Returns a reference to hash containing property names and values for
        a specified amino acid.

    GetAminoAcidPropertiesNames
            @Names = GetAminoAcidPropertiesNames([$Mode]);
            $NamesRef = GetAminoAcidPropertiesNames([$Mode]);

        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 *Mode*. Possible values for *Mode*:
        *Alphabetical or ByGroup*; Default: *ByGroup*

    GetAminoAcidPropertyName
            $Value = GetAminoAcid<PropertyName>($AminoAcidID);

        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 *property names*: 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

    GetAminoAcids
            $NamesRef = GetAminoAcids([$NameType]);
            (@Names) = GetAminoAcids([$NameType]);

        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
        *NameType*: *ThreeLetterCode, OneLetterCode, or AminoAcid*.

    IsAminoAcid
            $Status = IsAminoAcid($AminoAcidID);

        Returns a flag indicating whether or not its a known amino acid ID.

    IsAminoAcidProperty
            $Status = IsAminoAcid($PropertyName);

        Returns a flag indicating whether or not its a known amino acid
        property name.

AUTHOR
    Manish Sud <msud@san.rr.com>

SEE ALSO
    NucleicAcids.pm, PeriodicTable.pm

COPYRIGHT
    Copyright (C) 2015 Manish Sud. All rights reserved.

    This file is part of MayaChemTools.

    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.

