Used trait IsAminoAcid

rustyms-generate-imgt/src/structs.rs

@@ -4,7 +4,7 @@ use std::str::FromStr;
 
 use crate::imgt_gene::IMGTGene;
 use crate::shared::{AnnotatedSequence, Gene, Species};
-use rustyms::AminoAcid;
+use rustyms::{AminoAcid, IsAminoAcid};
 
 #[derive(Debug)]
 pub struct DataItem {
@@ -57,7 +57,12 @@ impl Display for Region {
             // self.found_seq.0,
             self.found_seq
                 .as_ref()
-                .map(|seq| seq.1 .0.iter().map(|a| a.char()).collect::<String>())
+                .map(|seq| seq
+                    .1
+                     .0
+                    .iter()
+                    .map(|a| a.pro_forma_definition())
+                    .collect::<String>())
                 .unwrap_or_else(|e| format!("<NO SEQ!>: {e}")),
         )
     }
@@ -237,7 +242,10 @@ impl std::fmt::Debug for AASequence {
         write!(
             f,
             "[{}]",
-            self.0.iter().map(|a| a.char()).collect::<String>()
+            self.0
+                .iter()
+                .map(|a| a.pro_forma_definition())
+                .collect::<String>()
         )
     }
 }

rustyms-py/src/lib.rs

@@ -6,7 +6,7 @@ use std::num::NonZeroU16;
 use ordered_float::OrderedFloat;
 use pyo3::{exceptions::PyValueError, prelude::*, types::PyType};
 
-use rustyms::{AnnotatableSpectrum, Chemical, Linked, MultiChemical};
+use rustyms::{AnnotatableSpectrum, Chemical, IsAminoAcid, Linked, MultiChemical};
 
 /// Mass mode enum.
 #[pyclass(eq, eq_int)]
@@ -440,7 +440,7 @@ impl AminoAcid {
     }
 
     fn __str__(&self) -> String {
-        self.0.char().to_string()
+        self.0.pro_forma_definition().to_string()
     }
 
     fn __repr__(&self) -> String {
@@ -1124,7 +1124,7 @@ impl Peptidoform {
         self.0
             .sequence()
             .iter()
-            .map(|x| x.aminoacid.char())
+            .map(|x| x.aminoacid.pro_forma_definition())
             .collect()
     }
 

rustyms/src/align/multi_alignment.rs

@@ -36,7 +36,7 @@ impl<Complexity> MultiAlignmentLine<'_, Complexity> {
         {
             print!(
                 "{}{}",
-                piece.1.aminoacid.char(),
+                piece.1.aminoacid,
                 "·".repeat(piece.0.step as usize - 1)
             );
         }

rustyms/src/checked_aminoacid.rs

@@ -3,7 +3,8 @@ use std::marker::PhantomData;
 use serde::{Deserialize, Serialize};
 
 use crate::{
-    AminoAcid, Chemical, MolecularFormula, Multi, MultiChemical, SemiAmbiguous, UnAmbiguous,
+    aminoacids::IsAminoAcid, AminoAcid, Chemical, MolecularFormula, Multi, MultiChemical,
+    SemiAmbiguous, UnAmbiguous,
 };
 
 /// A checked amino acid. This wraps an [`AminoAcid`] to keep track of the maximal complexity of
@@ -279,24 +280,48 @@ impl<T> CheckedAminoAcid<T> {
         self.aminoacid.canonical_identical(rhs.aminoacid)
     }
 
-    /// Get the description of the amino acid as a single character
-    pub const fn char(self) -> char {
-        self.aminoacid.char()
+    /// Get the underlying (unchecked) amino acid
+    pub const fn aminoacid(self) -> AminoAcid {
+        self.aminoacid
     }
+}
 
-    /// Get the 3 letter code for the amino acid
-    pub const fn code(self) -> &'static str {
-        self.aminoacid.code()
+impl<T> IsAminoAcid for CheckedAminoAcid<T> {
+    fn name(&self) -> std::borrow::Cow<'_, str> {
+        self.aminoacid.name()
     }
 
-    /// Get the full name of the amino acid
-    pub const fn name(self) -> &'static str {
-        self.aminoacid.name()
+    fn three_letter_code(&self) -> Option<std::borrow::Cow<'_, str>> {
+        self.aminoacid.three_letter_code()
     }
 
-    /// Get the underlying (unchecked) amino acid
-    pub const fn aminoacid(self) -> AminoAcid {
+    fn one_letter_code(&self) -> Option<char> {
+        self.aminoacid.one_letter_code()
+    }
+
+    fn pro_forma_definition(&self) -> std::borrow::Cow<'_, str> {
+        self.aminoacid.pro_forma_definition()
+    }
+
+    fn immonium_losses(&self) -> std::borrow::Cow<'_, [crate::NeutralLoss]> {
+        self.aminoacid.immonium_losses()
+    }
+
+    fn satellite_ion_fragments(
+        &self,
+        sequence_index: crate::SequencePosition,
+        peptidoform_index: usize,
+    ) -> Option<std::borrow::Cow<'_, Multi<MolecularFormula>>> {
         self.aminoacid
+            .satellite_ion_fragments(sequence_index, peptidoform_index)
+    }
+
+    fn side_chain(
+        &self,
+        sequence_index: crate::SequencePosition,
+        peptidoform_index: usize,
+    ) -> std::borrow::Cow<'_, Multi<MolecularFormula>> {
+        self.aminoacid.side_chain(sequence_index, peptidoform_index)
     }
 }
 
@@ -398,7 +423,7 @@ impl<T> Default for CheckedAminoAcid<T> {
 
 impl<T> std::fmt::Display for CheckedAminoAcid<T> {
     fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
-        write!(f, "{}", self.char())
+        write!(f, "{}", self.pro_forma_definition())
     }
 }
 

rustyms/src/fragment.rs

@@ -481,18 +481,16 @@ impl FragmentType {
             Self::z·(_) => Cow::Borrowed("z·"),
             Self::B(_) => Cow::Borrowed("B"),
             Self::Y(_) | Self::YComposition(_, _) => Cow::Borrowed("Y"),
-            Self::Diagnostic(DiagnosticPosition::Peptide(_, aa)) => {
-                Cow::Owned(format!("d{}", aa.char()))
-            }
+            Self::Diagnostic(DiagnosticPosition::Peptide(_, aa)) => Cow::Owned(format!("d{aa}")),
             Self::Diagnostic(DiagnosticPosition::Reporter) => Cow::Borrowed("r"),
             Self::Diagnostic(DiagnosticPosition::Labile(m)) => Cow::Owned(format!("d{m}")),
             Self::Diagnostic(
                 DiagnosticPosition::Glycan(_, sug)
                 | DiagnosticPosition::GlycanCompositional(sug, _),
             ) => Cow::Owned(format!("d{sug}")),
             Self::Oxonium(_) | Self::OxoniumComposition(_, _) => Cow::Borrowed("oxonium"),
-            Self::Immonium(_, aa) => Cow::Owned(format!("i{}", aa.aminoacid.char())),
-            Self::PrecursorSideChainLoss(_, aa) => Cow::Owned(format!("p-s{}", aa.char())),
+            Self::Immonium(_, aa) => Cow::Owned(format!("i{}", aa.aminoacid)),
+            Self::PrecursorSideChainLoss(_, aa) => Cow::Owned(format!("p-s{aa}")),
             Self::Precursor => Cow::Borrowed("p"),
             Self::Internal(fragmentation, _, _) => Cow::Owned(format!(
                 "m{}",

rustyms/src/lib.rs

@@ -85,7 +85,7 @@ pub use crate::sequence_element::SequenceElement;
 pub use crate::sequence_position::*;
 pub use crate::spectrum::{AnnotatableSpectrum, AnnotatedSpectrum, RawSpectrum};
 pub use crate::tolerance::*;
-pub use aminoacids::AminoAcid;
+pub use aminoacids::{AminoAcid, IsAminoAcid};
 pub use checked_aminoacid::CheckedAminoAcid;
 pub use fragment::Fragment;
 pub use peptidoform::{CompoundPeptidoformIon, Peptidoform, PeptidoformIon};

rustyms/src/sequence_element.rs

@@ -117,7 +117,7 @@ impl<T> SequenceElement<T> {
         if self.ambiguous.is_some() && last_ambiguous != self.ambiguous {
             write!(f, "(?")?;
         }
-        write!(f, "{}", self.aminoacid.char())?;
+        write!(f, "{}", self.aminoacid)?;
         for m in &self.modifications {
             let mut display_ambiguous = false;
             if let Modification::Ambiguous { id, .. } = m {