diff mayachemtools/docs/modules/man3/AminoAcids.3 @ 0:73ae111cf86f draft

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+.\" ========================================================================
+.\"
+.IX Title "AMINOACIDS 1"
+.TH AMINOACIDS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
+.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.if n .ad l
+.nh
+.SH "NAME"
+AminoAcids
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+use AminoAcids;
+.PP
+use AminoAcids qw(:all);
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+\&\fBAminoAcids\fR module provides the following functions:
+.PP
+GetAminoAcidPropertiesData, GetAminoAcidPropertiesNames, GetAminoAcid<PropertyName>,
+GetAminoAcids, IsAminoAcid, IsAminoAcidProperty
+.SH "FUNCTIONS"
+.IX Header "FUNCTIONS"
+.IP "\fBGetAminoAcidPropertiesData\fR" 4
+.IX Item "GetAminoAcidPropertiesData"
+.Vb 1
+\&    $DataHashRef = GetAminoAcidPropertiesData($AminoAcidID);
+.Ve
+.Sp
+Returns a reference to hash containing property names and values for a specified
+amino acid.
+.IP "\fBGetAminoAcidPropertiesNames\fR" 4
+.IX Item "GetAminoAcidPropertiesNames"
+.Vb 2
+\&    @Names = GetAminoAcidPropertiesNames([$Mode]);
+\&    $NamesRef = GetAminoAcidPropertiesNames([$Mode]);
+.Ve
+.Sp
+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
+\&\fIMode\fR. Possible values for \fIMode\fR: \fIAlphabetical or  ByGroup\fR; Default: \fIByGroup\fR
+.IP "\fBGetAminoAcidPropertyName\fR" 4
+.IX Item "GetAminoAcidPropertyName"
+.Vb 1
+\&    $Value = GetAminoAcid<PropertyName>($AminoAcidID);
+.Ve
+.Sp
+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 \s-1AUTOLOAD\s0
+funcion. Here is the list of known amino acids \fIproperty names\fR: DNACodons, RNACodons,
+AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint,
+pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O,
+MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), vanderWaalsVolume,
+\&\f(CW%AccessibleResidues\fR, \f(CW%BuriedResidues\fR, 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
+.IP "\fBGetAminoAcids\fR" 4
+.IX Item "GetAminoAcids"
+.Vb 2
+\&    $NamesRef = GetAminoAcids([$NameType]);
+\&    (@Names) = GetAminoAcids([$NameType]);
+.Ve
+.Sp
+Returns an array or a reference to an array containing names of amino acids
+as one letter code, three letter code, or amino acid name controlled by optional
+parameter \f(CW$NameType\fR. By default, amino acids names are returned as three
+letter code. Possible values for \fINameType\fR: \fIThreeLetterCode, OneLetterCode, or
+AminoAcid\fR.
+.IP "\fBIsAminoAcid\fR" 4
+.IX Item "IsAminoAcid"
+.Vb 1
+\&    $Status = IsAminoAcid($AminoAcidID);
+.Ve
+.Sp
+Returns a flag indicating whether or not its a known amino acid \s-1ID\s0.
+.IP "\fBIsAminoAcidProperty\fR" 4
+.IX Item "IsAminoAcidProperty"
+.Vb 1
+\&    $Status = IsAminoAcid($PropertyName);
+.Ve
+.Sp
+Returns a flag indicating whether or not its a known amino acid property name.
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+Manish Sud <[e-mail]>
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+NucleicAcids.pm, PeriodicTable.pm
+.SH "COPYRIGHT"
+.IX Header "COPYRIGHT"
+Copyright (C) 2015 Manish Sud. All rights reserved.
+.PP
+This file is part of MayaChemTools.
+.PP
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.