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## 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.

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