update: have all possiblities in config

src/py/mat3ra/made/tools/build/defect/configuration.py

@@ -36,23 +36,63 @@ class PointDefectConfiguration(BaseDefectConfiguration, InMemoryEntity):
     Args:
         crystal (Material): The Material object.
         defect_type (PointDefectTypeEnum): The type of the defect.
-        coordinate (List[float]): The crystal coordinate of the defect.
+        coordinate (Optional[List[float]]): The crystal coordinate of the defect.
+        approximate_coordinate (Optional[List[float]]): Approximate coordinate for the defect. Ignored, if coordinate is provided.
+        site_id (Optional[int]): The site ID for the defect in the crystal. Ignored, if coordinate is provided.
         chemical_element (Optional[str]): The chemical element.
     """
 
     defect_type: PointDefectTypeEnum
-    coordinate: List[float] = [0, 0, 0]
+    coordinate: Optional[List[float]] = None
+    approximate_coordinate: Optional[List[float]] = None
+    site_id: Optional[int] = None
     chemical_element: Optional[str] = None
     use_cartesian_coordinates: bool = False
 
+    def __init__(
+        self,
+        crystal: Material,
+        defect_type: PointDefectTypeEnum,
+        coordinate: Optional[List[float]] = None,
+        site_id: Optional[int] = None,
+        approximate_coordinate: Optional[List[float]] = None,
+        chemical_element: Optional[str] = None,
+        use_cartesian_coordinates: bool = False,
+    ):
+        if coordinate is not None:
+            self.crystal = crystal
+            self.defect_type = defect_type
+            self.coordinate = coordinate
+            self.chemical_element = chemical_element
+        elif site_id is not None:
+            self.from_site_id(
+                crystal=crystal, defect_type=defect_type, site_id=site_id, chemical_element=chemical_element
+            )
+        elif approximate_coordinate is not None:
+            self.from_approximate_coordinate(
+                crystal=crystal,
+                defect_type=defect_type,
+                approximate_coordinate=approximate_coordinate,
+                chemical_element=chemical_element,
+                use_cartesian_coordinates=use_cartesian_coordinates,
+            )
+        else:
+            raise ValueError("At least one of site_id, coordinate, or approximate_coordinate must be provided.")
+
     @classmethod
     def from_site_id(
         cls, crystal: Material, defect_type: PointDefectTypeEnum, site_id: int, chemical_element: Optional[str] = None
     ):
         if not crystal:
             raise RuntimeError("Crystal is not defined")
         coordinate = crystal.coordinates_array[site_id]
-        return cls(crystal=crystal, defect_type=defect_type, coordinate=coordinate, chemical_element=chemical_element)
+        return cls(
+            crystal=crystal,
+            defect_type=defect_type,
+            site_id=site_id,
+            coordinate=coordinate,
+            chemical_element=chemical_element,
+        )
 
     @classmethod
     def from_approximate_coordinate(
@@ -74,18 +114,6 @@ def from_approximate_coordinate(
             crystal=crystal, defect_type=defect_type, site_id=closest_site_id, chemical_element=chemical_element
         )
 
-    @classmethod
-    def from_dict(cls, crystal: Material, data: dict):
-        if "site_id" in data:
-            config = PointDefectConfiguration.from_site_id(crystal=crystal, **data)
-        elif "coordinate" in data:
-            config = PointDefectConfiguration(crystal=crystal, **data)
-        elif "approximate_coordinate" in data:
-            config = PointDefectConfiguration.from_approximate_coordinate(crystal=crystal, **data)
-        else:
-            raise ValueError(f"Invalid defect configuration: {data}")
-        return config
-
     @property
     def _json(self):
         return {

tests/py/unit/test_tools_build_defect.py

@@ -48,7 +48,7 @@ def test_create_substitution():
 def test_create_interstitial():
     # Interstitial Ge at 0.5, 0.5, 0.5 position
     configuration = PointDefectConfiguration(
-        crystal=clean_material, defect_type="interstitial", chemical_element="Ge", position=[0.5, 0.5, 0.5]
+        crystal=clean_material, defect_type="interstitial", chemical_element="Ge", coordinate=[0.5, 0.5, 0.5]
     )
     defect = create_defect(configuration)