Struct rustyms::LinearPeptide

pub struct LinearPeptide {
    pub global: Vec<(Element, u16)>,
    pub labile: Vec<Modification>,
    pub n_term: Option<Modification>,
    pub c_term: Option<Modification>,
    pub sequence: Vec<SequenceElement>,
    pub ambiguous_modifications: Vec<Vec<usize>>,
    pub charge_carriers: Option<MolecularCharge>,
}

A peptide with all data as provided by pro forma. Preferably generated by using the crate::ComplexPeptide::pro_forma function.

Fields

global: Vec<(Element, u16)>

Global isotope modifications, saved as the element and the species that all occurrence of that element will consist of. Eg (N, 15) will make all occurring nitrogens be isotope 15.

labile: Vec<Modification>

Labile modifications, which will not be found in the actual spectrum.

n_term: Option<Modification>

N terminal modification

c_term: Option<Modification>

C terminal modification

sequence: Vec<SequenceElement>

The sequence of this peptide (includes local modifications)

ambiguous_modifications: Vec<Vec<usize>>

For each ambiguous modification list all possible positions it can be placed on. Indexed by the ambiguous modification id.

charge_carriers: Option<MolecularCharge>

The adduct ions, if specified

Implementations

impl LinearPeptide

pub fn len(&self) -> usize

Get the number of amino acids making up this peptide

pub fn is_empty(&self) -> bool

Check if there are any amino acids in this peptide

pub fn n_term(&self) -> MolecularFormula

The mass of the N terminal modifications. The global isotope modifications are NOT applied.

pub fn c_term(&self) -> MolecularFormula

The mass of the C terminal modifications. The global isotope modifications are NOT applied.

pub fn reverse(&self) -> Self

Get the reverse of this peptide

pub fn formula(&self) -> Option<MolecularFormula>

Gives the formula for the whole peptide. With the global isotope modifications applied.

pub fn bare_formula(&self) -> Option<MolecularFormula>

Gives the formula for the whole peptide with no C and N terminal modifications. With the global isotope modifications applied.

pub fn generate_theoretical_fragments( &self, max_charge: Charge, model: &Model, peptide_index: usize ) -> Option<Vec<Fragment>>

Generate the theoretical fragments for this peptide, with the given maximal charge of the fragments, and the given model. With the global isotope modifications applied.

Panics

If max_charge outside the range 1..=u64::MAX.

Trait Implementations

impl Clone for LinearPeptide

fn clone(&self) -> LinearPeptide

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for LinearPeptide

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

Formats the value using the given formatter.

impl Default for LinearPeptide

fn default() -> LinearPeptide

Returns the “default value” for a type.

impl Display for LinearPeptide

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

Formats the value using the given formatter.

impl PartialEq for LinearPeptide

fn eq(&self, other: &LinearPeptide) -> 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 StructuralPartialEq for LinearPeptide