Merge pull request #120 from compomics/fix-sage-IM

Fix: restore compatibility with older Sage versions with no ion_mobility column present

Author: RalfG

psm_utils/io/sage.py

@@ -58,13 +58,8 @@ def _get_peptide_spectrum_match(self, psm_dict) -> PSM:
             except KeyError:
                 continue
 
-        # If ion mobility is not 0.0 (not present), add it to the rescoring features     
-        if float(psm_dict['ion_mobility']):
-            rescoring_features.update({
-            'ion_mobility': float(psm_dict['ion_mobility']),
-            'predicted_mobility': float(psm_dict['predicted_mobility']),
-            'delta_mobility': float(psm_dict['delta_mobility'])
-            })
+        ion_mobility_features = self._extract_ion_mobility_features(psm_dict)
+        rescoring_features.update(ion_mobility_features)
 
         return PSM(
             peptidoform=self._parse_peptidoform(
@@ -78,7 +73,7 @@ def _get_peptide_spectrum_match(self, psm_dict) -> PSM:
             score=float(psm_dict[self.score_column]),
             precursor_mz=self._parse_precursor_mz(psm_dict["expmass"], psm_dict["charge"]),
             retention_time=float(psm_dict["rt"]),
-            ion_mobility=float(psm_dict["ion_mobility"]) if float(psm_dict["ion_mobility"]) else None,
+            ion_mobility=rescoring_features.get("ion_mobility", None),
             protein_list=psm_dict["proteins"].split(";"),
             source="sage",
             rank=int(float(psm_dict["rank"])),
@@ -101,6 +96,24 @@ def _parse_precursor_mz(expmass: str, charge: Optional[str]) -> Optional[float]:
             return (expmass + (mass.nist_mass["H"][1][0] * charge)) / charge
         else:
             return None
+        
+    @staticmethod
+    def _extract_ion_mobility_features(psm_dict: dict) -> dict:
+        """
+        Extract ion mobility features from the PSM dictionary if present and non-zero.
+        Returns a dict with the relevant keys or an empty dict.
+        """
+        try:
+            ion_mob = float(psm_dict["ion_mobility"])
+            if ion_mob:
+                return {
+                    "ion_mobility": ion_mob,
+                    "predicted_mobility": float(psm_dict["predicted_mobility"]),
+                    "delta_mobility": float(psm_dict["delta_mobility"]),
+                }
+        except (KeyError, ValueError):
+            pass
+        return {}
 
     @classmethod
     def from_dataframe(cls, dataframe) -> PSMList: