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InfoAminoAcids.pl - List properties of amino acids
InfoAminoAcids.pl AminoAcidIDs...
InfoAminoAcids.pl [-h, --help] [--outdelim comma | tab | semicolon] [--output STDOUT | File] [--outputstyle AminoAcidBlock | AminoAcidRows] [-o, --overwrite] [--precision number] [--propertiesmode Categories | Names | All] [-p, --properties CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]] [--propertieslinting ByGroup | Alphabetical] [-q, --quote yes | no] [-r, --root rootname] [-w, --workingdir dirname] AminoAcidIDs...
List amino acid properties. Amino acids identification supports these three types of IDs: one letter code, three letter code or name. Amino acid properties data, in addition to basic information about amino acids - one and three letter codes, name, DNA and RNA codons, molecular weight - include variety of other properties: polarity, acidity, hydrophobicity, and so on.
AminoAcidIDs is a space delimited list of values to identify amino acids.
Input value format is: ThreeLetterCode [OneLetterCode AminoAcidName...]. Default: Ala. Examples:
Print this help message.
Output text file delimiter. Possible values: comma, tab, or semicolon Default value: comma.
List information at STDOUT or write it to a file. Possible values: STDOUT or File. Default: STDOUT. -r, --root option is used to generate output file name.
Specify how to list amino acid information: add a new line for each property and present it as a block for each amino acid; or include all properties in one line and show it as a single line.
Possible values: AminoAcidBlock | AminoAcidRows. Default: AminoAcidBlock
An example for AminoAcidBlock output style:
An example for AminoAcidRows output style:
Overwrite existing files.
Precision for listing numerical values. Default: up to 4 decimal places. Valid values: positive integers.
Specify how property names are specified: use category names; explicit list of property names; or use all available properties. Possible values: Categories, Names, or All. Default: Categories.
This option is used in conjunction with -p, --properties option to specify properties of interest.
This option is --propertiesmode specific. In general, it's a list of comma separated category or property names.
Specify which amino acid properties information to list for the amino acid IDs specified using command: line parameters: list basic and/or hydrophobicity information; list all available information; or specify a comma separated list of amino acid property names.
Possible values: Basic | BasicPlus | BasicAndHydrophobicity | BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]. Default: Basic.
Basic includes: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4
BasicPlus includes: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), LinearStructure, LinearStructureAtpH7.4
BasicAndHydrophobicity includes: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers
BasicAndHydrophobicityPlus includes: (ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, 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
Here is a complete list of available properties: ThreeLetterCode, OneLetterCode, AminoAcid, 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
Specify how to list properties for amino acids: group by category or an alphabetical by property names. Possible values: ByGroup or Alphabetical. Default: ByGroup.
Put quotes around column values in output text file. Possible values: yes or no. Default value: yes.
New text file name is generated using the root: <Root>.<Ext>. File name is only used during File value of -o, --output option.
Default file name: AminoAcidInfo<mode>.<Ext>. The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text files respectively.
Location of working directory. Default: current directory.
To list basic properties information for amino acid Ala, type:
To list all available properties information for amino acid Ala, type:
To list basic properties information for amino acids Ala, Arg, and Asp type:
To list all available properties information for amino acids Ala, Arg, and Asp type:
To list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp type:
To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight for amino acids Ala, Arg, and Asp type:
To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp in rows insetad of amino acid blocks with quotes around the values, type:
To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp in rows insetad of amino acid blocks with quotes around the values and write them into a file AminoAcidProperties.csv, type:
InfoNucleicAcids.plInfoPeriodicTableElements.pl
Copyright (C) 2024 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.
