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AminoAcids Module

Contains the AminoAcid type and its according functions. The AminoAcid type is a complex presentation of amino acids, allowing modifications

Types

Type Description

AminoAcid

Amino acid Codes

ParsedAminoAcidChar

Lexer tags for parsing AminoAcids

Functions and values

Function or value Description

aminoAcidSetAmbiguity

Full Usage: aminoAcidSetAmbiguity

Returns: Set<AminoAcid>

Set of all ambiguous codes

Returns: Set<AminoAcid>

aminoAcidSetGapTer

Full Usage: aminoAcidSetGapTer

Returns: Set<AminoAcid>

Set containing the Gap and the Terminator AminoAcid

Returns: Set<AminoAcid>

aminoAcidSetHydrophobic

Full Usage: aminoAcidSetHydrophobic

Returns: Set<AminoAcid>

Set of all AminoAcids with hydrophobic sidechain

Returns: Set<AminoAcid>

aminoAcidSetNegCharged

Full Usage: aminoAcidSetNegCharged

Returns: Set<AminoAcid>

Set of all AminoAcids with acidic sidechain

Returns: Set<AminoAcid>

aminoAcidSetPolarUncharged

Full Usage: aminoAcidSetPolarUncharged

Returns: Set<AminoAcid>

Set of all AminoAcids with uncharged polar sidechain

Returns: Set<AminoAcid>

aminoAcidSetPosCharged

Full Usage: aminoAcidSetPosCharged

Returns: Set<AminoAcid>

Set of all AminoAcids with basic (positively charged) sidechain

Returns: Set<AminoAcid>

aminoAcidSetProteinogenic

Full Usage: aminoAcidSetProteinogenic

Returns: Set<AminoAcid>

Set of all 22 proteinogenic amino acids (20 standard + Selenocysteine + Pyrrolysine)

Returns: Set<AminoAcid>

aminoAcidSetProteinogenicEucaryotes

Full Usage: aminoAcidSetProteinogenicEucaryotes

Returns: Set<AminoAcid>

Set of all 21 proteinogenic amino acids in eucaryotes (20 standard + Selenocysteine)

Returns: Set<AminoAcid>

aminoAcidSetSpecialCases

Full Usage: aminoAcidSetSpecialCases

Returns: Set<AminoAcid>
Returns: Set<AminoAcid>

aminoAcidSetStandard

Full Usage: aminoAcidSetStandard

Returns: Set<AminoAcid>

Set of the 20 standard amino acids of the genetic code

Returns: Set<AminoAcid>

averageMass aa

Full Usage: averageMass aa

Parameters:
Returns: float

Returns the average mass of AminoAcid (without H20)

aa : AminoAcid
Returns: float

charToParsedAminoAcidChar c

Full Usage: charToParsedAminoAcidChar c

Parameters:
    c : char

Returns: ParsedAminoAcidChar

Simple Lexer for parsing AminoAcids from chars. The full parser is located in the BioItemsConverter-module

c : char
Returns: ParsedAminoAcidChar

formula aa

Full Usage: formula aa

Parameters:
Returns: Formula

Returns amino acid formulas minus H20

aa : AminoAcid
Returns: Formula

getAminoAcidWithoutMod aa

Full Usage: getAminoAcidWithoutMod aa

Parameters:
Returns: AminoAcid

Gets amino acid without the modifications

aa : AminoAcid
Returns: AminoAcid

getModifications aa

Full Usage: getModifications aa

Parameters:
Returns: Modification list

Gets amino acid modifications

aa : AminoAcid
Returns: Modification list

initAverageMassWithMemP

Full Usage: initAverageMassWithMemP

Returns: AminoAcid -> float

Returns a function to calculate the average mass of a AminoAcid with memoization

Returns: AminoAcid -> float

initMonoisoMassWithMemP

Full Usage: initMonoisoMassWithMemP

Returns: AminoAcid -> float

Returns a function to calculate the monoisotopic mass of a AminoAcid with memoization

Returns: AminoAcid -> float

isCharged aa

Full Usage: isCharged aa

Parameters:
Returns: bool

Returns true, if the AminoAcid has a basic or acidic side chain

aa : AminoAcid
Returns: bool

isGap aa

Full Usage: isGap aa

Parameters:
Returns: bool

Returns true if AminoAcid represents a sequence gap

aa : AminoAcid
Returns: bool

isHydrophobic aa

Full Usage: isHydrophobic aa

Parameters:
Returns: bool

Returns true, if the AminoAcid has a hydrophobic side chain

aa : AminoAcid
Returns: bool

isModified aa

Full Usage: isModified aa

Parameters:
Returns: bool

Returns true if AminoAcid contains a modification

aa : AminoAcid
Returns: bool

isNegCharged aa

Full Usage: isNegCharged aa

Parameters:
Returns: bool

Returns true, if the AminoAcid has an acidic side chain

aa : AminoAcid
Returns: bool

isPolarUncharged aa

Full Usage: isPolarUncharged aa

Parameters:
Returns: bool

Returns true, if the AminoAcid has a polar, uncharged side chain

aa : AminoAcid
Returns: bool

isPosCharged aa

Full Usage: isPosCharged aa

Parameters:
Returns: bool

Returns true, if the AminoAcid has a basic side chain

aa : AminoAcid
Returns: bool

isTerminator aa

Full Usage: isTerminator aa

Parameters:
Returns: bool

Returns true if AminoAcid represents a sequence terminator

aa : AminoAcid
Returns: bool

isotopicLabelFunc aa f

Full Usage: isotopicLabelFunc aa f

Parameters:
Returns: Formula

Modifies a formula f by applying all isotopic modifications of a given amino acid aa

aa : AminoAcid
f : Formula
Returns: Formula

monoisoMass aa

Full Usage: monoisoMass aa

Parameters:
Returns: float

Returns the monoisotopic mass of AminoAcid (without H20)

aa : AminoAcid
Returns: float

name aa

Full Usage: name aa

Parameters:
Returns: string

Returns the name of AminoAcid

aa : AminoAcid
Returns: string

setModification md aa

Full Usage: setModification md aa

Parameters:
Returns: AminoAcid

Sets amino acid modification

md : Modification
aa : AminoAcid
Returns: AminoAcid

setModifications md aa

Full Usage: setModifications md aa

Parameters:
Returns: AminoAcid

Sets multiple amino acid modifications

md : Modification list
aa : AminoAcid
Returns: AminoAcid

symbol aa

Full Usage: symbol aa

Parameters:
Returns: char

Returns the symbol of AminoAcid

aa : AminoAcid
Returns: char

tryGetModifications aa

Full Usage: tryGetModifications aa

Parameters:
Returns: Modification list option

Gets amino acid modifications

aa : AminoAcid
Returns: Modification list option

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