Updated API based on align-cli and changed (multi)chemical to have bo…

…th 'formula(s)' and 'formula(s)_inner' for ease of use
snijderlab · Sep 10, 2024 · 292f7a4 · 292f7a4
1 parent 8887981
commit 292f7a4
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Showing 25 changed files with 258 additions and 215 deletions.
diff --git a/rustyms-py/src/lib.rs b/rustyms-py/src/lib.rs
@@ -459,7 +459,7 @@ impl AminoAcid {
     ///
     fn formulas(&self) -> Vec<MolecularFormula> {
         self.0
-            .formulas(SequencePosition::default(), 0)
+            .formulas()
             .iter()
             .map(|f| MolecularFormula(f.clone()))
             .collect()
@@ -474,13 +474,7 @@ impl AminoAcid {
     /// List[MolecularFormula]
     ///
     fn formula(&self) -> MolecularFormula {
-        MolecularFormula(
-            self.0
-                .formulas(SequencePosition::default(), 0)
-                .first()
-                .unwrap()
-                .clone(),
-        )
+        MolecularFormula(self.0.formulas().first().unwrap().clone())
     }
 
     /// Monoisotopic mass(es) of the amino acid.
@@ -493,7 +487,7 @@ impl AminoAcid {
     ///
     fn monoisotopic_masses(&self) -> Vec<f64> {
         self.0
-            .formulas(SequencePosition::default(), 0)
+            .formulas()
             .iter()
             .map(|f| f.monoisotopic_mass().value)
             .collect()
@@ -508,12 +502,7 @@ impl AminoAcid {
     /// float
     ///
     fn monoisotopic_mass(&self) -> f64 {
-        self.0
-            .formulas(SequencePosition::default(), 0)
-            .first()
-            .unwrap()
-            .monoisotopic_mass()
-            .value
+        self.0.formulas().first().unwrap().monoisotopic_mass().value
     }
 }
 
@@ -565,7 +554,7 @@ impl SimpleModification {
     /// MolecularFormula
     ///
     fn formula(&self) -> MolecularFormula {
-        MolecularFormula(self.0.formula(SequencePosition::default(), 0))
+        MolecularFormula(self.0.formula())
     }
 
     /// Monoisotopic mass of the modification.
@@ -575,10 +564,7 @@ impl SimpleModification {
     /// float
     ///
     fn monoisotopic_mass(&self) -> f64 {
-        self.0
-            .formula(SequencePosition::default(), 0)
-            .monoisotopic_mass()
-            .value
+        self.0.formula().monoisotopic_mass().value
     }
 }
 
@@ -1170,9 +1156,7 @@ impl LinearPeptide {
     ///
     #[getter]
     fn charge(&self) -> Option<isize> {
-        self.0
-            .get_charge_carriers()
-            .map(|c| c.formula(SequencePosition::default(), 0).charge().value)
+        self.0.get_charge_carriers().map(|c| c.charge().value)
     }
 
     /// The adduct ions, if specified.

diff --git a/rustyms/benches/iai.rs b/rustyms/benches/iai.rs
@@ -12,8 +12,7 @@ use iai_callgrind::{
 
 #[inline(never)]
 fn setup(a: &str, b: &str) -> (LinearPeptide<SimpleLinear>, LinearPeptide<SimpleLinear>) {
-    let _force_elements_init =
-        black_box(AminoAcid::Alanine.formulas(SequencePosition::default(), 0));
+    let _force_elements_init = black_box(AminoAcid::Alanine.formulas());
     (
         LinearPeptide::pro_forma(a, None)
             .unwrap()

diff --git a/rustyms/src/align/alignment.rs b/rustyms/src/align/alignment.rs
@@ -407,7 +407,7 @@ mod tests {
         align::{align, matrix::BLOSUM62, AlignType},
         peptide::SimpleLinear,
         system::da,
-        AminoAcid, LinearPeptide, MultiChemical, SequencePosition,
+        AminoAcid, LinearPeptide, MultiChemical,
     };
 
     #[test]
@@ -470,10 +470,8 @@ mod tests {
             .abs()
                 < f64::EPSILON
         );
-        let mass_diff_nd = (AminoAcid::Asparagine.formulas(SequencePosition::default(), 0)[0]
-            .monoisotopic_mass()
-            - AminoAcid::AsparticAcid.formulas(SequencePosition::default(), 0)[0]
-                .monoisotopic_mass())
+        let mass_diff_nd = (AminoAcid::Asparagine.formulas()[0].monoisotopic_mass()
+            - AminoAcid::AsparticAcid.formulas()[0].monoisotopic_mass())
         .value
         .abs();
         let mass_diff_bc = align::<1, SimpleLinear, SimpleLinear>(

diff --git a/rustyms/src/aminoacids.rs b/rustyms/src/aminoacids.rs
@@ -291,7 +291,7 @@ impl AminoAcid {
 
         if ions.a.0 && allow_terminal.0 {
             base_fragments.extend(Fragment::generate_all(
-                &(self.formulas(sequence_index, peptide_index)
+                &(self.formulas_inner(sequence_index, peptide_index)
                     * (modifications - molecular_formula!(H 1 C 1 O 1))),
                 peptidoform_index,
                 peptide_index,
@@ -304,7 +304,7 @@ impl AminoAcid {
         }
         if ions.b.0 && allow_terminal.0 {
             base_fragments.extend(Fragment::generate_all(
-                &(self.formulas(sequence_index, peptide_index)
+                &(self.formulas_inner(sequence_index, peptide_index)
                     * (modifications - molecular_formula!(H 1))),
                 peptidoform_index,
                 peptide_index,
@@ -317,7 +317,7 @@ impl AminoAcid {
         }
         if ions.c.0 && allow_terminal.0 {
             base_fragments.extend(Fragment::generate_all(
-                &(self.formulas(sequence_index, peptide_index)
+                &(self.formulas_inner(sequence_index, peptide_index)
                     * (modifications + molecular_formula!(H 2 N 1))),
                 peptidoform_index,
                 peptide_index,
@@ -332,7 +332,7 @@ impl AminoAcid {
             base_fragments.extend(Fragment::generate_all(
                 &(-self.satellite_ion_fragments(sequence_index, peptide_index)
                     * modifications
-                    * self.formulas(sequence_index, peptide_index)
+                    * self.formulas_inner(sequence_index, peptide_index)
                     + molecular_formula!(H 1 C 1 O 1)),
                 peptidoform_index,
                 peptide_index,
@@ -359,7 +359,7 @@ impl AminoAcid {
             base_fragments.extend(Fragment::generate_all(
                 &(-self.satellite_ion_fragments(sequence_index, peptide_index)
                     * modifications
-                    * self.formulas(sequence_index, peptide_index)
+                    * self.formulas_inner(sequence_index, peptide_index)
                     + molecular_formula!(H 2 N 1)),
                 peptidoform_index,
                 peptide_index,
@@ -372,7 +372,7 @@ impl AminoAcid {
         }
         if ions.x.0 && allow_terminal.1 {
             base_fragments.extend(Fragment::generate_all(
-                &(self.formulas(sequence_index, peptide_index)
+                &(self.formulas_inner(sequence_index, peptide_index)
                     * (modifications + molecular_formula!(C 1 O 1) - molecular_formula!(H 1))),
                 peptidoform_index,
                 peptide_index,
@@ -385,7 +385,7 @@ impl AminoAcid {
         }
         if ions.y.0 && allow_terminal.1 {
             base_fragments.extend(Fragment::generate_all(
-                &(self.formulas(sequence_index, peptide_index)
+                &(self.formulas_inner(sequence_index, peptide_index)
                     * (modifications + molecular_formula!(H 1))),
                 peptidoform_index,
                 peptide_index,
@@ -398,7 +398,7 @@ impl AminoAcid {
         }
         if ions.z.0 && allow_terminal.1 {
             base_fragments.extend(Fragment::generate_all(
-                &(self.formulas(sequence_index, peptide_index)
+                &(self.formulas_inner(sequence_index, peptide_index)
                     * (modifications - molecular_formula!(H 2 N 1))),
                 peptidoform_index,
                 peptide_index,
@@ -409,7 +409,7 @@ impl AminoAcid {
                 ions.z.2,
             ));
             base_fragments.extend(Fragment::generate_all(
-                &(self.formulas(sequence_index, peptide_index)
+                &(self.formulas_inner(sequence_index, peptide_index)
                     * (modifications - molecular_formula!(H 1 N 1))),
                 peptidoform_index,
                 peptide_index,
@@ -423,7 +423,7 @@ impl AminoAcid {
 
         if ions.immonium.0 && allow_terminal.0 && allow_terminal.1 {
             base_fragments.extend(Fragment::generate_all(
-                &(self.formulas(sequence_index, peptide_index)
+                &(self.formulas_inner(sequence_index, peptide_index)
                     * (modifications - molecular_formula!(C 1 O 1))),
                 peptidoform_index,
                 peptide_index,
@@ -567,21 +567,17 @@ mod tests {
 
     #[test]
     fn mass() {
-        let weight_ala =
-            AminoAcid::Alanine.formulas(SequencePosition::default(), 0)[0].average_weight();
-        let mass_ala =
-            AminoAcid::Alanine.formulas(SequencePosition::default(), 0)[0].monoisotopic_mass();
+        let weight_ala = AminoAcid::Alanine.formulas()[0].average_weight();
+        let mass_ala = AminoAcid::Alanine.formulas()[0].monoisotopic_mass();
         assert_ne!(weight_ala, mass_ala);
         assert!((weight_ala.value - 71.07793).abs() < 1e-5);
         assert!((mass_ala.value - 71.037113783).abs() < 1e-5);
     }
 
     #[test]
     fn mass_lysine() {
-        let weight_lys =
-            AminoAcid::Lysine.formulas(SequencePosition::default(), 0)[0].average_weight();
-        let mass_lys =
-            AminoAcid::Lysine.formulas(SequencePosition::default(), 0)[0].monoisotopic_mass();
+        let weight_lys = AminoAcid::Lysine.formulas()[0].average_weight();
+        let mass_lys = AminoAcid::Lysine.formulas()[0].monoisotopic_mass();
         assert_ne!(weight_lys, mass_lys);
         assert!((weight_lys.value - 128.17240999999999).abs() < 1e-5);
         assert!((mass_lys.value - 128.094963010536).abs() < 1e-5);
@@ -615,12 +611,8 @@ mod tests {
         for (aa, mono_mass, average_weight) in known {
             let aa = AminoAcid::try_from(*aa).unwrap();
             let (mono, weight) = (
-                aa.formulas(SequencePosition::default(), 0)[0]
-                    .monoisotopic_mass()
-                    .value,
-                aa.formulas(SequencePosition::default(), 0)[0]
-                    .average_weight()
-                    .value,
+                aa.formulas()[0].monoisotopic_mass().value,
+                aa.formulas()[0].average_weight().value,
             );
             println!(
                 "{}: {} {} {} {}",

diff --git a/rustyms/src/build/resid.rs b/rustyms/src/build/resid.rs
@@ -11,7 +11,7 @@ use super::{
     ontology_modification::{OntologyModification, OntologyModificationList},
     AminoAcid, ModData, Ontology, PlacementRule, Position,
 };
-use crate::{formula::MultiChemical, print, MolecularFormula, SequencePosition};
+use crate::{formula::MultiChemical, print, MolecularFormula};
 
 use roxmltree::*;
 
@@ -194,16 +194,10 @@ fn parse_resid(debug: bool) -> Vec<OntologyModification> {
                     continue 'entry;
                 }
                 let diff_formula = modification.formula.clone()
-                    - rule
-                        .0
-                        .single_formula(SequencePosition::default(), 0)
-                        .expect("B or Z used as target")
+                    - rule.0.single_formula().expect("B or Z used as target")
                     - rule
                         .1
-                        .map(|a| {
-                            a.single_formula(SequencePosition::default(), 0)
-                                .expect("B or Z used as target")
-                        })
+                        .map(|a| a.single_formula().expect("B or Z used as target"))
                         .unwrap_or_default();
                 if shared_formula.is_some_and(|s| s != diff_formula) {
                     print(

diff --git a/rustyms/src/checked_aminoacid.rs b/rustyms/src/checked_aminoacid.rs
@@ -302,7 +302,7 @@ impl<T> CheckedAminoAcid<T> {
 
 impl Chemical for CheckedAminoAcid<UnAmbiguous> {
     /// Get all possible formula for an unambiguous amino acid (X is defined to be an empty formula)
-    fn formula(
+    fn formula_inner(
         &self,
         _sequence_index: crate::SequencePosition,
         _peptide_index: usize,
@@ -340,7 +340,7 @@ impl Chemical for CheckedAminoAcid<UnAmbiguous> {
 impl<T> MultiChemical for CheckedAminoAcid<T> {
     /// # Panics
     /// Is the sequence index is a terminal index
-    fn formulas(
+    fn formulas_inner(
         &self,
         sequence_index: crate::SequencePosition,
         peptide_index: usize,
@@ -361,7 +361,7 @@ impl<T> MultiChemical for CheckedAminoAcid<T> {
             ]
             .into(),
             _ => unreachable!(),        }
-        }, |unambiguous| unambiguous.formula(sequence_index, peptide_index).into())
+        }, |unambiguous| unambiguous.formula_inner(sequence_index, peptide_index).into())
     }
 }
 

diff --git a/rustyms/src/formula.rs b/rustyms/src/formula.rs
@@ -191,7 +191,7 @@ impl std::fmt::Display for MolecularFormula {
 mod tests {
     use crate::{
         model::ChargeRange, molecular_formula, AminoAcid, Fragment, MolecularCharge,
-        MolecularFormula, MultiChemical, SequencePosition,
+        MolecularFormula, MultiChemical,
     };
 
     #[test]
@@ -295,7 +295,7 @@ mod tests {
     #[test]
     #[allow(clippy::similar_names)]
     fn labels() {
-        let labelled = AminoAcid::AmbiguousAsparagine.formulas(SequencePosition::default(), 0);
+        let labelled = AminoAcid::AmbiguousAsparagine.formulas();
         let unlabelled: crate::Multi<MolecularFormula> =
             vec![molecular_formula!(C 1), molecular_formula!(H 1)].into();
         let mut mul_assign_l = labelled.clone();

diff --git a/rustyms/src/fragment.rs b/rustyms/src/fragment.rs
@@ -92,7 +92,7 @@ impl Fragment {
             .map(|(((term, mass), charge), loss)| Self {
                 formula: term
                     + mass
-                    + charge.formula(SequencePosition::default(), peptide_index)
+                    + charge.formula_inner(SequencePosition::default(), peptide_index)
                     + loss.unwrap_or(&NeutralLoss::Gain(MolecularFormula::default())),
                 charge: Charge::new::<crate::system::e>(charge.charge().value.try_into().unwrap()),
                 ion: annotation.clone(),
@@ -109,10 +109,8 @@ impl Fragment {
     #[must_use]
     fn with_charge(&self, charge: &MolecularCharge) -> Self {
         let formula = charge
-            .formula(SequencePosition::default(), 0)
-            .with_labels(&[AmbiguousLabel::ChargeCarrier(
-                charge.formula(SequencePosition::default(), 0),
-            )]);
+            .formula()
+            .with_labels(&[AmbiguousLabel::ChargeCarrier(charge.formula())]);
         let c = Charge::new::<crate::system::charge::e>(
             usize::try_from(formula.charge().value).unwrap(),
         );
@@ -605,7 +603,7 @@ mod tests {
     #[test]
     fn neutral_loss() {
         let a = Fragment::new(
-            AminoAcid::AsparticAcid.formulas(SequencePosition::default(), 0)[0].clone(),
+            AminoAcid::AsparticAcid.formulas()[0].clone(),
             Charge::new::<crate::system::charge::e>(1),
             0,
             0,