Moved amino acids predefined selection to AminoAcid

snijderlab · Nov 10, 2023 · bdd1e06 · bdd1e06
1 parent ee75c49
commit bdd1e06
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Showing 2 changed files with 50 additions and 26 deletions.
diff --git a/src/aminoacids.rs b/src/aminoacids.rs
@@ -101,6 +101,55 @@ impl AminoAcid {
     pub const Tyr: Self = Self::Tyrosine;
     pub const Xaa: Self = Self::Unknown;
 
+    /// All amino acids with a unique mass (no I/L in favour of J, no B, no Z, and no X)
+    pub const UNIQUE_MASS_AMINOACIDS: &[Self] = &[
+        Self::Glycine,
+        Self::Alanine,
+        Self::Arginine,
+        Self::Asparagine,
+        Self::AsparticAcid,
+        Self::Cysteine,
+        Self::Glutamine,
+        Self::GlutamicAcid,
+        Self::Histidine,
+        Self::AmbiguousLeucine,
+        Self::Lysine,
+        Self::Methionine,
+        Self::Phenylalanine,
+        Self::Proline,
+        Self::Serine,
+        Self::Threonine,
+        Self::Tryptophan,
+        Self::Tyrosine,
+        Self::Valine,
+        Self::Selenocysteine,
+        Self::Pyrrolysine,
+    ];
+
+    /// All 20 canonical amino acids
+    pub const CANONICAL_AMINOACIDS: &[Self] = &[
+        Self::Glycine,
+        Self::Alanine,
+        Self::Arginine,
+        Self::Asparagine,
+        Self::AsparticAcid,
+        Self::Cysteine,
+        Self::Glutamine,
+        Self::GlutamicAcid,
+        Self::Histidine,
+        Self::Leucine,
+        Self::Isoleucine,
+        Self::Lysine,
+        Self::Methionine,
+        Self::Phenylalanine,
+        Self::Proline,
+        Self::Serine,
+        Self::Threonine,
+        Self::Tryptophan,
+        Self::Tyrosine,
+        Self::Valine,
+    ];
+
     // TODO: Take side chain mutations into account (maybe define pyrrolysine as a mutation)
     pub fn satellite_ion_fragments(&self) -> Vec<MolecularFormula> {
         match self {

diff --git a/src/isobaric_sets.rs b/src/isobaric_sets.rs
@@ -521,31 +521,6 @@ impl Iterator for IsobaricSetIterator {
     }
 }
 
-/// All amino acids with a unique mass (no I/L in favour of J, no B, no Z, and no X)
-pub const UNIQUE_MASS_AMINOACIDS: &[AminoAcid] = &[
-    AminoAcid::Glycine,
-    AminoAcid::Alanine,
-    AminoAcid::Arginine,
-    AminoAcid::Asparagine,
-    AminoAcid::AsparticAcid,
-    AminoAcid::Cysteine,
-    AminoAcid::Glutamine,
-    AminoAcid::GlutamicAcid,
-    AminoAcid::Histidine,
-    AminoAcid::AmbiguousLeucine,
-    AminoAcid::Lysine,
-    AminoAcid::Methionine,
-    AminoAcid::Phenylalanine,
-    AminoAcid::Proline,
-    AminoAcid::Serine,
-    AminoAcid::Threonine,
-    AminoAcid::Tryptophan,
-    AminoAcid::Tyrosine,
-    AminoAcid::Valine,
-    AminoAcid::Selenocysteine,
-    AminoAcid::Pyrrolysine,
-];
-
 #[cfg(test)]
 mod tests {
     use crate::ComplexPeptide;
@@ -557,7 +532,7 @@ mod tests {
         let sets: Vec<LinearPeptide> = find_isobaric_sets(
             pep.bare_formula().unwrap().monoisotopic_mass().unwrap(),
             MassTolerance::Ppm(10.0),
-            UNIQUE_MASS_AMINOACIDS,
+            AminoAcid::UNIQUE_MASS_AMINOACIDS,
             &[],
             &[],
             None,