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1 NAME
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2 AminoAcids
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3
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4 SYNOPSIS
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5 use AminoAcids;
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6
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7 use AminoAcids qw(:all);
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8
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9 DESCRIPTION
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10 AminoAcids module provides the following functions:
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11
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12 GetAminoAcidPropertiesData, GetAminoAcidPropertiesNames,
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13 GetAminoAcid<PropertyName>, GetAminoAcids, IsAminoAcid,
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14 IsAminoAcidProperty
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15
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16 FUNCTIONS
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17 GetAminoAcidPropertiesData
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18 $DataHashRef = GetAminoAcidPropertiesData($AminoAcidID);
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19
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20 Returns a reference to hash containing property names and values for
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21 a specified amino acid.
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22
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23 GetAminoAcidPropertiesNames
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24 @Names = GetAminoAcidPropertiesNames([$Mode]);
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25 $NamesRef = GetAminoAcidPropertiesNames([$Mode]);
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26
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27 Returns an array or a reference to an array containing names of
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28 amino acids properties. Order of amino acids properties is
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29 controlled by optional parameter *Mode*. Possible values for *Mode*:
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30 *Alphabetical or ByGroup*; Default: *ByGroup*
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31
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32 GetAminoAcidPropertyName
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33 $Value = GetAminoAcid<PropertyName>($AminoAcidID);
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34
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35 Returns amino acid property value for a specified amino acid. These
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36 functions are not defined in this modules; these are implemented on
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37 the fly using Perl's AUTOLOAD funcion. Here is the list of known
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38 amino acids *property names*: DNACodons, RNACodons, AcidicBasic,
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39 PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic,
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40 IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight,
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41 ExactMass, ChemicalFormulaMinusH2O,
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42 MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056),
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43 vanderWaalsVolume, %AccessibleResidues, %BuriedResidues,
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44 AlphaHelixChouAndFasman, AlphaHelixDeleageAndRoux, AlphaHelixLevitt,
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45 AminoAcidsComposition, AminoAcidsCompositionInSwissProt,
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46 AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility,
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47 BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt,
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48 BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt,
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49 Bulkiness, CoilDeleageAndRoux, HPLCHFBARetention,
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50 HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4, HPLCTFARetention,
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51 HydrophobicityAbrahamAndLeo, HydrophobicityBlack,
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52 HydrophobicityBullAndBreese, HydrophobicityChothia,
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53 HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers,
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54 HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan,
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55 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers,
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56 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods,
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57 HydrophobicityJanin, HydrophobicityKyteAndDoolittle,
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58 HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers,
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59 HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos,
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60 HydrophobicityRfMobility, HydrophobicityRoseAndOthers,
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61 HydrophobicityRoseman, HydrophobicityWellingAndOthers,
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62 HydrophobicityWolfendenAndOthers, ParallelBetaStrand,
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63 PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide,
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64 RecognitionFactors, Refractivity, RelativeMutability,
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65 TotalBetaStrand, LinearStructure, LinearStructureAtpH7.4
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66
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67 GetAminoAcids
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68 $NamesRef = GetAminoAcids([$NameType]);
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69 (@Names) = GetAminoAcids([$NameType]);
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70
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71 Returns an array or a reference to an array containing names of
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72 amino acids as one letter code, three letter code, or amino acid
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73 name controlled by optional parameter $NameType. By default, amino
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74 acids names are returned as three letter code. Possible values for
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75 *NameType*: *ThreeLetterCode, OneLetterCode, or AminoAcid*.
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76
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77 IsAminoAcid
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78 $Status = IsAminoAcid($AminoAcidID);
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79
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80 Returns a flag indicating whether or not its a known amino acid ID.
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81
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82 IsAminoAcidProperty
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83 $Status = IsAminoAcid($PropertyName);
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84
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85 Returns a flag indicating whether or not its a known amino acid
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86 property name.
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87
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88 AUTHOR
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89 Manish Sud <msud@san.rr.com>
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90
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91 SEE ALSO
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92 NucleicAcids.pm, PeriodicTable.pm
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93
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94 COPYRIGHT
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95 Copyright (C) 2015 Manish Sud. All rights reserved.
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96
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97 This file is part of MayaChemTools.
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98
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99 MayaChemTools is free software; you can redistribute it and/or modify it
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100 under the terms of the GNU Lesser General Public License as published by
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101 the Free Software Foundation; either version 3 of the License, or (at
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102 your option) any later version.
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103
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