Updated python documentation and bindings for #52

docs/python/source/index.md

@@ -17,7 +17,7 @@ Python bindings are provided to several core components of the rustyms library,
 - {py:class}`~rustyms.Fragment` Theoretical fragment ion
 - {py:class}`~rustyms.SequenceElement` One position in a peptide sequence with amino acid and
   modifications
-- {py:class}`~rustyms.LinearPeptide` Peptide sequence, modifications, and charge, using
+- {py:class}`~rustyms.CompoundPeptidoformIon` Peptide sequence, modifications, and charge, using
   [ProForma 2.0](https://proforma.readthedocs.io) (see {ref}`ProForma support` for more
   information)
 - {py:class}`~rustyms.RawPeak` A single peak in a mass spectrum
@@ -43,7 +43,7 @@ raw_spectrum = rustyms.RawSpectrum(
 )
 
 # Create a new peptide from a ProForma 2.0 string
-peptide = rustyms.LinearPeptide("ACDE/2")
+peptide = rustyms.CompoundPeptidoformIon("ACDE/2")
 
 # Annotate the spectrum with the peptide
 annotated_spectrum = raw_spectrum.annotate(peptide, "cid_hcd")
@@ -68,7 +68,6 @@ rustyms Python bindings.
 :maxdepth: 2
 
 About <self>
-proforma-support
 api
 contributing
 ```

rustyms-py/src/lib.rs

@@ -347,7 +347,7 @@ impl MolecularFormula {
     }
 }
 
-/// A selection of ions that together define the charge of a peptide.
+/// A selection of ions that together define the charge of a peptidoform.
 #[pyclass]
 pub struct MolecularCharge(rustyms::MolecularCharge);
 
@@ -608,7 +608,7 @@ impl Modification {
     }
 }
 
-/// A theoretical fragment of a peptide.
+/// A theoretical fragment of a peptidoform.
 #[pyclass]
 #[derive(Debug)]
 pub struct Fragment(rustyms::Fragment);
@@ -660,7 +660,7 @@ impl Fragment {
         FragmentType(self.0.ion.clone())
     }
 
-    /// The peptide this fragment comes from, saved as the index into the list of peptides in the overarching crate::ComplexPeptide struct.
+    /// The peptidoform this fragment comes from, saved as the index into the list of peptidoforms in the overarching crate::PeptidoformIon struct.
     ///
     /// Returns
     /// -------
@@ -671,7 +671,7 @@ impl Fragment {
         self.0.peptidoform_index
     }
 
-    /// The peptidoform this fragment comes from, saved as the index into the list of peptides in the overarching crate::ComplexPeptide struct.
+    /// The peptidoform ion this fragment comes from, saved as the index into the list of peptidoform ions in the overarching crate::CompoundPeptidoformIon struct.
     ///
     /// Returns
     /// -------
@@ -827,7 +827,7 @@ impl SequencePosition {
         matches!(self, SequencePosition(rustyms::SequencePosition::CTerm))
     }
 }
-/// A compound peptidoform with all data as provided by ProForma 2.0.
+/// A compound peptidoform ion with all data as provided by ProForma 2.0.
 ///
 /// Parameters
 /// ----------
@@ -836,46 +836,46 @@ impl SequencePosition {
 ///
 #[pyclass]
 #[derive(Clone)]
-pub struct CompoundPeptidoform(rustyms::CompoundPeptidoformIon);
+pub struct CompoundPeptidoformIon(rustyms::CompoundPeptidoformIon);
 
 #[pymethods]
-impl CompoundPeptidoform {
-    /// Create a new peptide from a ProForma string.
+impl CompoundPeptidoformIon {
+    /// Create a new compound peptidoform ion from a ProForma string.
     #[new]
     fn new(proforma: &str) -> Result<Self, CustomError> {
         rustyms::CompoundPeptidoformIon::pro_forma(proforma, None)
-            .map(CompoundPeptidoform)
+            .map(CompoundPeptidoformIon)
             .map_err(CustomError)
     }
 
-    /// Create a new peptide from a peptidoform.
+    /// Create a new compound peptidoform ion from a peptidoform ion.
     #[staticmethod]
-    fn from_peptidoform(peptidoform: Peptidoform) -> Self {
-        CompoundPeptidoform(peptidoform.0.into())
+    fn from_peptidoform_ion(peptidoform: PeptidoformIon) -> Self {
+        CompoundPeptidoformIon(peptidoform.0.into())
     }
 
-    /// Create a new peptide from a linear peptide.
+    /// Create a new compound peptidoform ion from a peptidoform.
     #[staticmethod]
-    fn from_peptide(peptide: LinearPeptide) -> Self {
-        CompoundPeptidoform(peptide.0.into())
+    fn from_peptidoform(peptidoform: Peptidoform) -> Self {
+        CompoundPeptidoformIon(peptidoform.0.into())
     }
 
-    /// Get all peptidoforms making up this compound peptidoform.
+    /// Get all peptidoform ions making up this compound peptidoform.
     ///
     /// Returns
     /// -------
-    /// List[Peptidoform]
+    /// List[PeptidoformIon]
     ///
     #[getter]
-    fn peptidoforms(&self) -> Vec<Peptidoform> {
+    fn peptidoform_ions(&self) -> Vec<PeptidoformIon> {
         self.0
             .peptidoform_ions()
             .iter()
-            .map(|p| Peptidoform(p.clone()))
+            .map(|p| PeptidoformIon(p.clone()))
             .collect()
     }
 
-    /// Generate the theoretical fragments for this compound peptidoform, with the given maximal charge of the fragments,
+    /// Generate the theoretical fragments for this compound peptidoform ion, with the given maximal charge of the fragments,
     /// and the given model. With the global isotope modifications applied.
     ///
     /// Parameters
@@ -911,15 +911,15 @@ impl CompoundPeptidoform {
     }
 
     fn __repr__(&self) -> String {
-        format!("CompoundPeptidoform({})", self.0)
+        format!("CompoundPeptidoformIon({})", self.0)
     }
 
     fn __len__(&self) -> usize {
         self.0.peptidoform_ions().len()
     }
 }
 
-/// A peptidoform with all data as provided by ProForma 2.0.
+/// A peptidoform ion with all data as provided by ProForma 2.0.
 ///
 /// Parameters
 /// ----------
@@ -928,40 +928,40 @@ impl CompoundPeptidoform {
 ///
 #[pyclass]
 #[derive(Clone)]
-pub struct Peptidoform(rustyms::PeptidoformIon);
+pub struct PeptidoformIon(rustyms::PeptidoformIon);
 
 #[pymethods]
-impl Peptidoform {
-    /// Create a new peptidoform from a ProForma string. Panics
+impl PeptidoformIon {
+    /// Create a new peptidoform ion from a ProForma string. Panics
     #[new]
     fn new(proforma: &str) -> Result<Self, CustomError> {
         rustyms::PeptidoformIon::pro_forma(proforma, None)
-            .map(Peptidoform)
+            .map(PeptidoformIon)
             .map_err(CustomError)
     }
 
-    /// Create a new peptidoform from a linear peptide.
+    /// Create a new peptidoform ion from a peptidoform.
     #[staticmethod]
-    fn from_peptide(peptide: LinearPeptide) -> Self {
-        Peptidoform(peptide.0.clone().into())
+    fn from_peptidoform(peptidoform: Peptidoform) -> Self {
+        PeptidoformIon(peptidoform.0.clone().into())
     }
 
-    /// Get all peptides making up this peptidoform.
+    /// Get all peptidoforms making up this peptidoform ion.
     ///
     /// Returns
     /// -------
-    /// List[LinearPeptide]
+    /// List[Peptidoform]
     ///
     #[getter]
-    fn peptides(&self) -> Vec<LinearPeptide> {
+    fn peptidoforms(&self) -> Vec<Peptidoform> {
         self.0
             .peptidoforms()
             .iter()
-            .map(|p| LinearPeptide(p.clone()))
+            .map(|p| Peptidoform(p.clone()))
             .collect()
     }
 
-    /// Generate the theoretical fragments for this peptidoform, with the given maximal charge of the fragments,
+    /// Generate the theoretical fragments for this peptidoform ion, with the given maximal charge of the fragments,
     /// and the given model. With the global isotope modifications applied.
     ///
     /// Parameters
@@ -997,15 +997,15 @@ impl Peptidoform {
     }
 
     fn __repr__(&self) -> String {
-        format!("Peptidoform({})", self.0)
+        format!("PeptidoformIon({})", self.0)
     }
 
     fn __len__(&self) -> usize {
         self.0.peptidoforms().len()
     }
 }
 
-/// A peptide with all data as provided by ProForma 2.0.
+/// A peptidoform with all data as provided by ProForma 2.0.
 ///
 /// Parameters
 /// ----------
@@ -1014,15 +1014,15 @@ impl Peptidoform {
 ///
 #[pyclass]
 #[derive(Clone)]
-pub struct LinearPeptide(rustyms::Peptidoform<Linked>);
+pub struct Peptidoform(rustyms::Peptidoform<Linked>);
 
 #[pymethods]
-impl LinearPeptide {
-    /// Create a new peptide from a ProForma string.
+impl Peptidoform {
+    /// Create a new peptidoform from a ProForma string.
     #[new]
     fn new(proforma: &str) -> Result<Self, CustomError> {
         rustyms::Peptidoform::pro_forma(proforma, None)
-            .map(LinearPeptide)
+            .map(Peptidoform)
             .map_err(CustomError)
     }
 
@@ -1031,7 +1031,7 @@ impl LinearPeptide {
     }
 
     fn __repr__(&self) -> String {
-        format!("LinearPeptide({})", self.0)
+        format!("Peptidoform({})", self.0)
     }
 
     fn __len__(&self) -> usize {
@@ -1083,7 +1083,7 @@ impl LinearPeptide {
             .collect()
     }
 
-    /// Sequence of the peptide including modifications.
+    /// Sequence of the peptidoform including modifications.
     ///
     /// Returns
     /// -------
@@ -1128,7 +1128,7 @@ impl LinearPeptide {
             .collect()
     }
 
-    /// The precursor charge of the peptide.
+    /// The precursor charge of the peptidoform.
     ///
     /// Returns
     /// -------
@@ -1152,17 +1152,17 @@ impl LinearPeptide {
             .map(|c| MolecularCharge(c.clone()))
     }
 
-    /// Get a copy of the peptide with its sequence reversed.
+    /// Get a copy of the peptidoform with its sequence reversed.
     ///
     /// Returns
     /// -------
-    /// LinearPeptide
+    /// Peptidoform
     ///
-    fn reverse(&self) -> LinearPeptide {
-        LinearPeptide(self.0.reverse())
+    fn reverse(&self) -> Peptidoform {
+        Peptidoform(self.0.reverse())
     }
 
-    /// Gives the formulas for the whole peptide. With the global isotope modifications applied. (Any B/Z will result in multiple possible formulas.)
+    /// Gives the formulas for the whole peptidoform. With the global isotope modifications applied. (Any B/Z will result in multiple possible formulas.)
     ///
     /// Returns
     /// -------
@@ -1177,7 +1177,7 @@ impl LinearPeptide {
         })
     }
 
-    /// Generate the theoretical fragments for this peptide, with the given maximal charge of the fragments, and the given model. With the global isotope modifications applied.
+    /// Generate the theoretical fragments for this peptidoform, with the given maximal charge of the fragments, and the given model. With the global isotope modifications applied.
     ///
     /// Parameters
     /// ----------
@@ -1479,12 +1479,12 @@ impl RawSpectrum {
         self.0.clone().into_iter().map(RawPeak).collect()
     }
 
-    /// Annotate this spectrum with the given peptide
+    /// Annotate this spectrum with the given peptidoform
     ///
     /// Parameters
     /// ----------
-    /// peptide : CompoundPeptide
-    ///     The peptide to annotate the spectrum with.
+    /// peptidoform : CompoundPeptidoformIon
+    ///     The peptidoform to annotate the spectrum with.
     /// model : FragmentationModel
     ///     The model to use for the fragmentation.
     /// mode : MassMode
@@ -1500,22 +1500,22 @@ impl RawSpectrum {
     /// ValueError
     ///     If the model is not one of the valid models.
     ///
-    #[pyo3(signature = (peptide, model, mode=&MassMode::Monoisotopic))]
+    #[pyo3(signature = (peptidoform, model, mode=&MassMode::Monoisotopic))]
     fn annotate(
         &self,
-        peptide: CompoundPeptidoform,
+        peptidoform: CompoundPeptidoformIon,
         model: &FragmentationModel,
         mode: &MassMode,
     ) -> PyResult<AnnotatedSpectrum> {
         let rusty_model = match_model(model)?;
-        let fragments = peptide.0.generate_theoretical_fragments(
+        let fragments = peptidoform.0.generate_theoretical_fragments(
             self.0
                 .charge
                 .unwrap_or(rustyms::system::usize::Charge::new::<rustyms::system::e>(1)),
             &rusty_model,
         );
         Ok(AnnotatedSpectrum(self.0.annotate(
-            peptide.0,
+            peptidoform.0,
             &fragments,
             &rusty_model,
             match mode {
@@ -1622,18 +1622,18 @@ fn rustyms_py03(_py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_class::<AminoAcid>()?;
     m.add_class::<AnnotatedPeak>()?;
     m.add_class::<AnnotatedSpectrum>()?;
-    m.add_class::<CompoundPeptidoform>()?;
+    m.add_class::<CompoundPeptidoformIon>()?;
     m.add_class::<CustomError>()?;
     m.add_class::<Element>()?;
     m.add_class::<Fragment>()?;
     m.add_class::<FragmentationModel>()?;
     m.add_class::<FragmentType>()?;
-    m.add_class::<LinearPeptide>()?;
+    m.add_class::<Peptidoform>()?;
     m.add_class::<MassMode>()?;
     m.add_class::<Modification>()?;
     m.add_class::<MolecularCharge>()?;
     m.add_class::<MolecularFormula>()?;
-    m.add_class::<Peptidoform>()?;
+    m.add_class::<PeptidoformIon>()?;
     m.add_class::<RawPeak>()?;
     m.add_class::<RawSpectrum>()?;
     m.add_class::<SequenceElement>()?;

rustyms/src/identification/fasta.rs

@@ -29,6 +29,18 @@ pub struct FastaData {
     annotations: Vec<(Annotation, usize)>,
 }
 
+impl std::cmp::Ord for FastaData {
+    fn cmp(&self, other: &Self) -> std::cmp::Ordering {
+        self.line_index.cmp(&other.line_index)
+    }
+}
+
+impl std::cmp::PartialOrd for FastaData {
+    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
+        Some(self.cmp(other))
+    }
+}
+
 impl AnnotatedPeptide for FastaData {
     type Complexity = SemiAmbiguous;
     fn peptide(&self) -> &Peptidoform<SemiAmbiguous> {