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