mzcore 0.2.0

Core logic for handling massspectrometry in Rust.
Documentation 
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//! Module used to create the [`IsAminoAcid`] trait

use std::borrow::Cow;

use crate::{
    chemistry::{MolecularFormula, SatelliteLabel},
    quantities::Multi,
    sequence::SequencePosition,
};

/// A general trait to define amino acids.
pub trait IsAminoAcid {
    /// The full name for this amino acid.
    fn name(&self) -> Cow<'_, str>;
    /// The three letter code for this amino acid. Or None if there is no common three letter
    /// definition for this amino acid.
    fn three_letter_code(&self) -> Option<Cow<'_, str>>;
    /// The one letter code for this amino acid. Or None if there is no common single character
    /// definition for this amino acid.
    #[doc(alias = "code")]
    fn one_letter_code(&self) -> Option<char>;
    /// The ProForma definition for this amino acid. If this is not a simple amino acid it can be
    /// defined as an amino acid with an additional modification. For example `X[H9C2N2]` could be
    /// used if Arginine was not defined as `R` in ProForma.
    fn pro_forma_definition(&self) -> Cow<'_, str>;
    /// The molecular formula of the side chain of the amino acid. The `sequence_index` and
    /// `peptidoform_index` are used to keep track of ambiguous amino acids.
    fn side_chain(
        &self,
        sequence_index: SequencePosition,
        peptidoform_index: usize,
        peptidoform_ion_index: usize,
    ) -> Cow<'_, Multi<MolecularFormula>>;
    /// The molecular formulas that can fragment for satellite ions (d and w). Commonly the fragment
    /// after the second carbon into the side chain. `MolecularFormula::default()` can be returned
    /// if no satellite ions are possible. The `sequence_index` and `peptidoform_index` are used to
    /// keep track of ambiguous amino acids.
    fn satellite_ion_fragments(
        &self,
        sequence_index: SequencePosition,
        peptidoform_index: usize,
        peptidoform_ion_index: usize,
    ) -> Option<Cow<'_, [(SatelliteLabel, MolecularFormula)]>>;
}