AminoAcids (BioFSharp)

AminoAcids Module

Namespace: BioFSharp
Assembly: BioFSharp.dll

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
`ambiguousSet` Full Usage: `ambiguousSet` Returns: `Set<AminoAcid>`	Set of all ambiguous codes Returns: `Set<AminoAcid>`
`averageMass aa` Full Usage: `averageMass aa` Parameters: aa : `AminoAcid` Returns: `float`	Returns the average mass of AminoAcid (without H20) aa : `AminoAcid` Returns: `float`
`formula aa` Full Usage: `formula aa` Parameters: aa : `AminoAcid` Returns: `Formula`	Returns amino acid formulas minus H20 aa : `AminoAcid` Returns: `Formula`
`gapTerSet` Full Usage: `gapTerSet` Returns: `Set<AminoAcid>`	Set containing the Gap and the Terminator AminoAcid Returns: `Set<AminoAcid>`
`getAminoAcidWithoutMod aa` Full Usage: `getAminoAcidWithoutMod aa` Parameters: aa : `AminoAcid` Returns: `AminoAcid`	Gets amino acid without the modifications aa : `AminoAcid` Returns: `AminoAcid`
`getModifications aa` Full Usage: `getModifications aa` Parameters: aa : `AminoAcid` Returns: `Modification list`	Gets amino acid modifications aa : `AminoAcid` Returns: `Modification list`
`hydrophobicSet` Full Usage: `hydrophobicSet` Returns: `Set<AminoAcid>`	Set of all AminoAcids with hydrophobic sidechain Returns: `Set<AminoAcid>`
`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: aa : `AminoAcid` 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: aa : `AminoAcid` Returns: `bool`	Returns true if AminoAcid represents a sequence gap aa : `AminoAcid` Returns: `bool`
`isHydrophobic aa` Full Usage: `isHydrophobic aa` Parameters: aa : `AminoAcid` Returns: `bool`	Returns true, if the AminoAcid has a hydrophobic side chain aa : `AminoAcid` Returns: `bool`
`isModified aa` Full Usage: `isModified aa` Parameters: aa : `AminoAcid` Returns: `bool`	Returns true if AminoAcid contains a modification aa : `AminoAcid` Returns: `bool`
`isNegCharged aa` Full Usage: `isNegCharged aa` Parameters: aa : `AminoAcid` Returns: `bool`	Returns true, if the AminoAcid has an acidic side chain aa : `AminoAcid` Returns: `bool`
`isPolarUncharged aa` Full Usage: `isPolarUncharged aa` Parameters: aa : `AminoAcid` Returns: `bool`	Returns true, if the AminoAcid has a polar, uncharged side chain aa : `AminoAcid` Returns: `bool`
`isPosCharged aa` Full Usage: `isPosCharged aa` Parameters: aa : `AminoAcid` Returns: `bool`	Returns true, if the AminoAcid has a basic side chain aa : `AminoAcid` Returns: `bool`
`isTerminator aa` Full Usage: `isTerminator aa` Parameters: aa : `AminoAcid` Returns: `bool`	Returns true if AminoAcid represents a sequence terminator aa : `AminoAcid` Returns: `bool`
`isotopicLabelFunc aa f` Full Usage: `isotopicLabelFunc aa f` Parameters: aa : `AminoAcid` f : `Formula` 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: aa : `AminoAcid` Returns: `float`	Returns the monoisotopic mass of AminoAcid (without H20) aa : `AminoAcid` Returns: `float`
`name aa` Full Usage: `name aa` Parameters: aa : `AminoAcid` Returns: `string`	Returns the name of AminoAcid aa : `AminoAcid` Returns: `string`
`negativelyChargedSet` Full Usage: `negativelyChargedSet` Returns: `Set<AminoAcid>`	Set of all AminoAcids with acidic sidechain Returns: `Set<AminoAcid>`
`parseOneLetterCode letter` Full Usage: `parseOneLetterCode letter` Parameters: letter : `char` Returns: `ParsedAminoAcidChar`	Simple Lexer for parsing AminoAcids from chars. The full parser is located in the BioItemsConverter-module letter : `char` Returns: `ParsedAminoAcidChar`
`parseThreeLetterCode letters` Full Usage: `parseThreeLetterCode letters` Parameters: letters : `'a` Returns: `ParsedAminoAcidChar`	letters : `'a` Returns: `ParsedAminoAcidChar`
`polarUnchargedSet` Full Usage: `polarUnchargedSet` Returns: `Set<AminoAcid>`	Set of all AminoAcids with uncharged polar sidechain Returns: `Set<AminoAcid>`
`positivelyChargedSet` Full Usage: `positivelyChargedSet` Returns: `Set<AminoAcid>`	Set of all AminoAcids with basic (positively charged) sidechain Returns: `Set<AminoAcid>`
`proteinogenicInEucariotesSet` Full Usage: `proteinogenicInEucariotesSet` Returns: `Set<AminoAcid>`	Set of all 21 proteinogenic amino acids in eucaryotes (20 standard + Selenocysteine) Returns: `Set<AminoAcid>`
`proteinogenicSet` Full Usage: `proteinogenicSet` Returns: `Set<AminoAcid>`	Set of all 22 proteinogenic amino acids (20 standard + Selenocysteine + Pyrrolysine) Returns: `Set<AminoAcid>`
`setModification md aa` Full Usage: `setModification md aa` Parameters: md : `Modification` aa : `AminoAcid` Returns: `AminoAcid`	Sets amino acid modification md : `Modification` aa : `AminoAcid` Returns: `AminoAcid`
`setModifications md aa` Full Usage: `setModifications md aa` Parameters: md : `Modification list` aa : `AminoAcid` Returns: `AminoAcid`	Sets multiple amino acid modifications md : `Modification list` aa : `AminoAcid` Returns: `AminoAcid`
`specialCasesSet` Full Usage: `specialCasesSet` Returns: `Set<AminoAcid>`	Returns: `Set<AminoAcid>`
`standardSet` Full Usage: `standardSet` Returns: `Set<AminoAcid>`	Set of the 20 standard amino acids of the genetic code Returns: `Set<AminoAcid>`
`symbol aa` Full Usage: `symbol aa` Parameters: aa : `AminoAcid` Returns: `char`	Returns the symbol of AminoAcid aa : `AminoAcid` Returns: `char`
`tryGetModifications aa` Full Usage: `tryGetModifications aa` Parameters: aa : `AminoAcid` Returns: `Modification list option`	Gets amino acid modifications aa : `AminoAcid` Returns: `Modification list option`