Enum rustyms::AminoAcid

pub enum AminoAcid {
    Alanine = 0,
    Arginine = 1,
    Asparagine = 2,
    AsparticAcid = 3,
    Cysteine = 4,
    Glutamine = 5,
    GlutamicAcid = 6,
    Glycine = 7,
    Histidine = 8,
    Isoleucine = 9,
    Leucine = 10,
    Lysine = 11,
    Methionine = 12,
    Phenylalanine = 13,
    Proline = 14,
    Serine = 15,
    Threonine = 16,
    Tryptophan = 17,
    Tyrosine = 18,
    Valine = 19,
    AmbiguousAsparagine = 20,
    AmbiguousLeucine = 21,
    AmbiguousGlutamine = 22,
    Selenocysteine = 23,
    Pyrrolysine = 24,
    Unknown = 25,
}

An amino acid, alongside the standard ones some ambiguous (B/J/Z/X) and non-standard (U/O) are included.

Variants

Alanine = 0

Arginine = 1

Asparagine = 2

AsparticAcid = 3

Cysteine = 4

Glutamine = 5

GlutamicAcid = 6

Glycine = 7

Histidine = 8

Isoleucine = 9

Leucine = 10

Lysine = 11

Methionine = 12

Phenylalanine = 13

Proline = 14

Serine = 15

Threonine = 16

Tryptophan = 17

Tyrosine = 18

Valine = 19

AmbiguousAsparagine = 20

AmbiguousLeucine = 21

AmbiguousGlutamine = 22

Selenocysteine = 23

Pyrrolysine = 24

Unknown = 25

Implementations

impl AminoAcid

All amino acid property classes according to IMGT.

IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties

Christelle Pommié, Séverine Levadoux, Robert Sabatier, Gérard Lefranc, Marie-Paule Lefranc

https://doi.org/10.1002/jmr.647

Adapted to include J,B,Z,U,O, and X.

pub const fn physiochemical_class(self) -> PhysiochemicalClass

pub const fn chemical_class(self) -> ChemicalClass

pub const fn volume_class(self) -> VolumeClass

pub const fn hydropathy_class(self) -> HydropathyClass

pub const fn charge_class(self) -> ChargeClass

pub const fn polarity_class(self) -> PolarityClass

pub const fn hydrogen_bond_class(self) -> HydrogenBondClass

impl AminoAcid

pub const TOTAL_NUMBER: usize = 26usize

The total number of amino acids

pub fn from_dna(dna: &str) -> Result<Option<Self>, NotACodon>

Translate the dna codon into the corresponding amino acid according to the standard DNA codon table. It returns None for a stop codon. https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables

Errors

It returns Err(NotACodon) when the given codon is not a valid dna codon.

impl AminoAcid

pub const A: Self = Self::Alanine

pub const B: Self = Self::AmbiguousAsparagine

pub const C: Self = Self::Cysteine

pub const D: Self = Self::AsparticAcid

pub const E: Self = Self::GlutamicAcid

pub const F: Self = Self::Phenylalanine

pub const G: Self = Self::Glycine

pub const H: Self = Self::Histidine

pub const I: Self = Self::Isoleucine

pub const J: Self = Self::AmbiguousLeucine

pub const K: Self = Self::Lysine

pub const L: Self = Self::Leucine

pub const M: Self = Self::Methionine

pub const N: Self = Self::Asparagine

pub const O: Self = Self::Pyrrolysine

pub const P: Self = Self::Proline

pub const Q: Self = Self::Glutamine

pub const R: Self = Self::Arginine

pub const S: Self = Self::Serine

pub const T: Self = Self::Threonine

pub const U: Self = Self::Selenocysteine

pub const V: Self = Self::Valine

pub const W: Self = Self::Tryptophan

pub const X: Self = Self::Unknown

pub const Y: Self = Self::Tyrosine

pub const Z: Self = Self::AmbiguousGlutamine

pub const Ala: Self = Self::Alanine

pub const Cys: Self = Self::Cysteine

pub const Asn: Self = Self::Asparagine

pub const Asp: Self = Self::AsparticAcid

pub const Asx: Self = Self::AmbiguousAsparagine

pub const Glu: Self = Self::GlutamicAcid

pub const Phe: Self = Self::Phenylalanine

pub const Gly: Self = Self::Glycine

pub const His: Self = Self::Histidine

pub const Ile: Self = Self::Isoleucine

pub const Xle: Self = Self::AmbiguousLeucine

pub const Lys: Self = Self::Lysine

pub const Leu: Self = Self::Leucine

pub const Met: Self = Self::Methionine

pub const Pyl: Self = Self::Pyrrolysine

pub const Pro: Self = Self::Proline

pub const Gln: Self = Self::Glutamine

pub const Glx: Self = Self::AmbiguousGlutamine

pub const Arg: Self = Self::Arginine

pub const Ser: Self = Self::Serine

pub const Thr: Self = Self::Threonine

pub const Sec: Self = Self::Selenocysteine

pub const Val: Self = Self::Valine

pub const Trp: Self = Self::Tryptophan

pub const Tyr: Self = Self::Tyrosine

pub const Xaa: Self = Self::Unknown

pub const UNIQUE_MASS_AMINO_ACIDS: &'static [Self] = _

All amino acids with a unique mass (no I/L in favour of J, no B, no Z, and no X)

pub const CANONICAL_AMINO_ACIDS: &'static [Self] = _

All 20 canonical amino acids

pub fn satellite_ion_fragments(self) -> Multi<MolecularFormula>

pub fn fragments( self, n_term: &[(MolecularFormula, String)], c_term: &[(MolecularFormula, String)], modifications: &MolecularFormula, charge_carriers: &MolecularCharge, sequence_index: usize, sequence_length: usize, ions: &PossibleIons<'_>, peptide_index: usize ) -> Vec<Fragment>

pub const fn char(self) -> char

pub fn canonical_identical(self, rhs: Self) -> bool

Check if two amino acids are considered identical. X is identical to anything, J to IL, B to ND, Z to EQ.

Trait Implementations

impl Clone for AminoAcid

fn clone(&self) -> AminoAcid

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for AminoAcid

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for AminoAcid

fn default() -> AminoAcid

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for AminoAcid

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl FromStr for AminoAcid

type Err = ()

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self, Self::Err>

Parses a string s to return a value of this type.

impl Hash for AminoAcid

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl MultiChemical for AminoAcid

fn formulas(&self) -> Multi<MolecularFormula>

Get all possible formulas for an amino acid (has one for all except B/Z has two for these)

fn charge(&self) -> Option<i16>

Get the charge of this chemical, it returns None if no charge is defined.

impl Ord for AminoAcid

fn cmp(&self, other: &AminoAcid) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized + PartialOrd,

Restrict a value to a certain interval.

impl PartialEq for AminoAcid

fn eq(&self, other: &AminoAcid) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for AminoAcid

fn partial_cmp(&self, other: &AminoAcid) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

This method tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

This method tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

This method tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

This method tests greater than or equal to (for self and other) and is used by the >= operator.

impl Serialize for AminoAcid

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl TryFrom<&str> for AminoAcid

type Error = ()

The type returned in the event of a conversion error.

fn try_from(value: &str) -> Result<Self, Self::Error>

Performs the conversion.

impl TryFrom<&u8> for AminoAcid

type Error = ()

The type returned in the event of a conversion error.

fn try_from(value: &u8) -> Result<Self, Self::Error>

Performs the conversion.

impl TryFrom<char> for AminoAcid

type Error = ()

The type returned in the event of a conversion error.

fn try_from(value: char) -> Result<Self, Self::Error>

Performs the conversion.

impl TryFrom<u8> for AminoAcid

type Error = ()

The type returned in the event of a conversion error.

fn try_from(value: u8) -> Result<Self, Self::Error>

Performs the conversion.

impl Copy for AminoAcid

impl Eq for AminoAcid

impl StructuralPartialEq for AminoAcid