API docs as jn

aiida_atomistic/data/structure/properties/per_site/charge.py → aiida_atomistic/data/structure/properties/intra_site/charge.py

@@ -12,7 +12,7 @@ class Charge(BaseProperty):
     """
     The charge property. 
     """
-    domain = "per-site"
+    domain = "intra-site"
     default_kind_threshold = 0.45
     # units... maybe specify in the docs.
     value: List[float] = Field(default=None)

aiida_atomistic/data/structure/properties/per_site/mass.py → aiida_atomistic/data/structure/properties/intra_site/mass.py

@@ -13,7 +13,7 @@ class Mass(BaseProperty):
     """
     The mass property. 
     """
-    domain = "per-site"
+    domain = "intra-site"
     default_kind_threshold = 1e-3
     # units... maybe specify in the docs.
     value: List[float] = Field(default=None)

aiida_atomistic/data/structure/properties/per_site/position.py → aiida_atomistic/data/structure/properties/intra_site/position.py

@@ -9,7 +9,7 @@ class Positions(BaseProperty):
     """
     The sites property. 
     """
-    domain = "per-site"
+    domain = "intra-site"
     #kind_threshold: float = Field(default=1e-3)
     value: List[Tuple[float,float,float]] = Field(default=None)
     kind_tags: List[str] = Field(default=None)   # thgis should be in position class? Unified, I think so. tipo alla fine del to kind fai un check e resetti.

aiida_atomistic/data/structure/properties/per_site/symbols.py → aiida_atomistic/data/structure/properties/intra_site/symbols.py

@@ -13,7 +13,7 @@ class Symbols(BaseProperty):
     """
     The symbols property, intended as the chemical symbols for each atom(site). 
     """
-    domain = "per-site"
+    domain = "intra-site"
     # units... maybe specify in the docs.
     value: List[Literal[_valid_symbols]]
 

aiida_atomistic/data/structure/properties/property_collector.py

@@ -6,10 +6,10 @@
 from aiida_atomistic.data.structure.properties.globals.cell import Cell
 from aiida_atomistic.data.structure.properties.globals.pbc import Pbc
 
-from aiida_atomistic.data.structure.properties.per_site.position import Positions
-from aiida_atomistic.data.structure.properties.per_site.symbols import Symbols
-from aiida_atomistic.data.structure.properties.per_site.mass import Mass
-from aiida_atomistic.data.structure.properties.per_site.charge import Charge
+from aiida_atomistic.data.structure.properties.intra_site.position import Positions
+from aiida_atomistic.data.structure.properties.intra_site.symbols import Symbols
+from aiida_atomistic.data.structure.properties.intra_site.mass import Mass
+from aiida_atomistic.data.structure.properties.intra_site.charge import Charge
 
 from aiida_atomistic.data.structure.properties.custom import CustomProperty
 
@@ -72,8 +72,9 @@ def __init__(
         self._inspect_properties(properties)
 
 
-    def get_valid_properties(self,):
+    """def get_supported_properties(self,):
         return list(typing.get_type_hints(self.__class__).keys())
+    """
 
     def get_property_attribute(self, key):
         # In AiiDA this could be self.base.attrs['properties'][key] or similar
@@ -86,11 +87,11 @@ def _inspect_properties(self,properties):
         have a defined prefix.
         """
         for pname,pvalue in properties.items():
-            if pname not in self.get_valid_properties():
-                raise NotImplementedError(f"Property '{pname}' is not yet supported.\nSupported properties are: {self.get_valid_properties()}")
+            if pname not in self.get_supported_properties():
+                raise NotImplementedError(f"Property '{pname}' is not yet supported.\nSupported properties are: {self.get_supported_properties()}")
             # custom properties:
-            #elif pname in self.get_valid_properties():
-            #    raise NotImplementedError(f"Property '{pname}' is not yet supported.\nSupported properties are: {self.get_valid_properties()}")
+            #elif pname in self.get_supported_properties():
+            #    raise NotImplementedError(f"Property '{pname}' is not yet supported.\nSupported properties are: {self.get_supported_properties()}")
             elif not pvalue:
                 raise ValueError(f"Property '{pname}' has not value provided.")
             elif len(pvalue)==0:

aiida_atomistic/data/structure/properties/property_utils.py

@@ -154,14 +154,14 @@ def _database_wise_setter(self, pname, pvalue):
         self._parent.base.attributes.set("_property_attributes",property_attributes)
         return
 
-    def get_valid_properties(self):
+    def get_supported_properties(self):
         # Get the implemented properties
-        return self._valid_properties.copy()
+        return list(self._valid_properties.copy())
 
-    def get_defined_properties(self):
+    def get_stored_properties(self):
         # Get the properties that you already set
         property_attributes = self._parent.base.attributes.get("_property_attributes")
-        return list(set(self.get_valid_properties()).intersection(
+        return list(set(self.get_supported_properties()).intersection(
             property_attributes.keys()
         ))
 

aiida_atomistic/data/structure/structure.py

@@ -783,14 +783,13 @@ def properties(self):
     @properties.setter
     def properties(self,value):
         raise AttributeError("After the initialization, `properties` is a read-only attribute")
-
-
+
     def to_dict(self):
         """ 
         Returns a dictionary with the properties defined.
         Used to generate new StructureData with some changed/updated properties.
         """
-        return self.base.attributes.get('_property_attributes')
+        return copy.deepcopy(self.base.attributes.get('_property_attributes'))
 
 
     def get_kinds(self, use_kind_tag = False, use_kind_name = True):
@@ -830,9 +829,9 @@ def get_kinds(self, use_kind_tag = False, use_kind_name = True):
         # Step 1:
         kind_properties = []
         kinds_values = {}
-        for single_property in self.properties.get_defined_properties():
+        for single_property in self.properties.get_stored_properties():
             prop = getattr(self.properties,single_property)
-            if prop.domain == "per-site" and not single_property in ["symbols","positions"]:
+            if prop.domain == "intra-site" and not single_property in ["symbols","positions"]:
                 kinds_per_property = prop.to_kinds()
                 kind_properties.append(kinds_per_property[0])
                 kinds_values[single_property] = kinds_per_property[1]