Comments based on review and start on AA trait

rustyms/src/aminoacids.rs

@@ -5,9 +5,44 @@ use crate::{
     fragment::{Fragment, FragmentType, PeptidePosition},
     model::*,
     molecular_charge::CachedCharge,
-    Multi, MultiChemical, NeutralLoss, SequencePosition,
+    system::Mass,
+    MassMode, Multi, MultiChemical, NeutralLoss, SequencePosition,
 };
 
+use std::borrow::Cow;
+
+// TODO: document
+pub trait IsAminoAcid {
+    fn name(&self) -> Cow<'_, str>;
+    fn three_letter_code(&self) -> Option<Cow<'_, str>>;
+    #[doc(alias = "code")]
+    fn one_letter_code(&self) -> Option<char>;
+    fn pro_forma_definition(&self) -> Cow<'_, str>;
+    fn formulas(&self) -> Cow<'_, Multi<MolecularFormula>>;
+    fn monoisotopic_mass(&self) -> Cow<'_, Multi<Mass>> {
+        Cow::Owned(
+            self.formulas()
+                .iter()
+                .map(MolecularFormula::monoisotopic_mass)
+                .collect(),
+        )
+    }
+    fn average_weight(&self) -> Cow<'_, Multi<Mass>> {
+        Cow::Owned(
+            self.formulas()
+                .iter()
+                .map(MolecularFormula::average_weight)
+                .collect(),
+        )
+    }
+    fn mass(&self, mode: MassMode) -> Cow<'_, Multi<Mass>> {
+        Cow::Owned(self.formulas().iter().map(|f| f.mass(mode)).collect())
+    }
+    fn side_chain(&self) -> Cow<'_, Multi<MolecularFormula>>;
+    fn satellite_ion_fragments(&self) -> Option<Cow<'_, Multi<MolecularFormula>>>;
+    fn immonium_losses(&self) -> Cow<'_, [NeutralLoss]>;
+}
+
 include!("shared/aminoacid.rs");
 
 impl AminoAcid {

rustyms/src/modification.rs

@@ -133,7 +133,6 @@ impl Chemical for SimpleModificationInner {
 
 impl SimpleModificationInner {
     /// Get a url for more information on this modification. Only defined for modifications from ontologies.
-    #[expect(clippy::missing_panics_doc)]
     pub fn ontology_url(&self) -> Option<String> {
         match self {
             Self::Mass(_) | Self::Formula(_) | Self::Glycan(_) | Self::GlycanStructure(_) => None,
@@ -593,9 +592,7 @@ impl Modification {
             Self::Ambiguous { modification, .. } => modification.formula(),
         }
     }
-}
 
-impl Modification {
     /// Check if this is a simple modification
     pub const fn simple(&self) -> Option<&SimpleModification> {
         match self {
@@ -613,7 +610,6 @@ impl Modification {
     }
 
     /// Get a url for more information on this modification. Only defined for modifications from ontologies.
-    #[expect(clippy::missing_panics_doc)]
     pub fn ontology_url(&self) -> Option<String> {
         match self {
             Self::Simple(modification)

rustyms/src/neutral_loss.rs

@@ -11,6 +11,9 @@ use crate::{
 include!("shared/neutral_loss.rs");
 
 impl NeutralLoss {
+    // TODO: extend with full list from annotator, plus figure out a way to make them const
+    //const WATER_LOSS: Self = Self::Loss(molecular_formula!(H 2 O 1));
+
     /// Check if this neutral loss if empty (has an empty molecular formula)
     pub fn is_empty(&self) -> bool {
         match self {

rustyms/src/peptidoform/parse.rs

@@ -72,7 +72,6 @@ impl PeptidoformIon {
     ///
     /// # Errors
     /// It fails when the string is not a valid ProForma string. Or when the string has multiple peptidoforms.
-    #[expect(clippy::too_many_lines)]
     pub fn pro_forma(
         value: &str,
         custom_database: Option<&CustomDatabase>,
@@ -96,7 +95,6 @@ impl CompoundPeptidoformIon {
     ///
     /// # Errors
     /// It fails when the string is not a valid ProForma string.
-    #[expect(clippy::too_many_lines)]
     pub fn pro_forma(
         value: &str,
         custom_database: Option<&CustomDatabase>,

rustyms/src/shared/modification.rs

@@ -31,6 +31,7 @@ pub enum Modification {
     },
 }
 
+// TODO: document what the usizes mean
 /// Indicate the cross-link side
 #[derive(Clone, PartialEq, Eq, Debug, Serialize, Deserialize)]
 pub enum CrossLinkSide {