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

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.