add pyresidue class

This class is a single amino acid, wrapper around Residue object

Author: jcharkow

openms_python/__init__.py

@@ -30,6 +30,7 @@
 from .py_consensusmap import Py_ConsensusMap
 from .py_experimentaldesign import Py_ExperimentalDesign
 from .py_aasequence import Py_AASequence
+from .py_residue import Py_Residue
 from .py_identifications import (
     ProteinIdentifications,
     PeptideIdentifications,
@@ -109,6 +110,7 @@ def get_example(name: str, *, load: bool = False, target_dir: Union[str, Path, N
     "Py_ConsensusMap",
     "Py_ExperimentalDesign",
     "Py_AASequence",
+    "Py_Residue",
     "ProteinIdentifications",
     "PeptideIdentifications",
     "Identifications",

openms_python/py_aasequence.py

@@ -5,6 +5,7 @@
 from typing import Optional, Literal
 import pyopenms as oms
 import warnings
+from .py_residue import Py_Residue
 
 
 class Py_AASequence:
@@ -242,20 +243,20 @@ def __getitem__(self, index):
             if step != 1:
                 raise ValueError("Step slicing is not supported for amino acid sequences")
             return Py_AASequence.from_native(self._sequence.getSubsequence(start, stop - start))
-        else:
+        else: # isinstance(index, int)
             # Handle negative indices
             if index < 0:
                 index = len(self) + index
             if index >= len(self):
                 raise IndexError(f"Index {index} out of range for sequence of length {len(self)}")
-            residue = self._sequence.getSubsequence(index, 1)
-            return Py_AASequence.from_native(residue)
+            residue = self._sequence.getResidue(index)
+            return Py_Residue.from_native(residue)
 
     def __iter__(self):
         """Iterate over residues."""
         for i in range(len(self)):
             yield self[i]
-    def __add__(self, other: Py_AASequence | str) -> Py_AASequence:
+    def __add__(self, other: Py_AASequence | str | Py_Residue) -> Py_AASequence:
         """
         Concatenate sequences.
 
@@ -279,6 +280,8 @@ def __add__(self, other: Py_AASequence | str) -> Py_AASequence:
             combined_str = self.sequence + other.sequence
         elif isinstance(other, str):
             combined_str = self.sequence + other
+        elif isinstance(other, Py_Residue):
+            combined_str = self.sequence + other.one_letter_code
         else:
             return NotImplemented
         return Py_AASequence.from_string(combined_str)
@@ -296,6 +299,9 @@ def __radd__(self, other: str) -> Py_AASequence:
         if isinstance(other, str):
             combined_str = other + self.sequence
             return Py_AASequence.from_string(combined_str)
+        if isinstance(other, Py_Residue):
+            combined_str = other.one_letter_code + self.sequence
+            return Py_AASequence.from_string(combined_str)
         return NotImplemented
 
     def __mul__(self, times: int) -> Py_AASequence: