musica 0.12.0__cp310-cp310-win32.whl → 0.12.2__cp310-cp310-win32.whl

musica/mechanism_configuration/tunneling.py

@@ -1,12 +1,17 @@
-from typing import Optional, Any, Dict, List, Union, Tuple
-from musica import _Tunneling, _ReactionComponent
-from .phase import Phase
-from .species import Species
+from .utils import _add_other_properties
 from .reactions import ReactionComponentSerializer
-from .utils import _add_other_properties, _remove_empty_keys
+from .species import Species
+from .phase import Phase
+from typing import Optional, Any, Dict, List, Union, Tuple
+from .. import backend
+
+_backend = backend.get_backend()
+_Tunneling = _backend._mechanism_configuration._Tunneling
+_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
+ReactionType = _backend._mechanism_configuration._ReactionType
 
 
-class Tunneling(_Tunneling):
+class Tunneling:
     """
     A class representing a quantum tunneling reaction rate constant.
 
@@ -37,7 +42,8 @@ class Tunneling(_Tunneling):
         A: Optional[float] = None,
         B: Optional[float] = None,
         C: Optional[float] = None,
-        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        reactants: Optional[List[Union[Species,
+                                       Tuple[float, Species]]]] = None,
         products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
         gas_phase: Optional[Phase] = None,
         other_properties: Optional[Dict[str, Any]] = None,
@@ -55,49 +61,190 @@ class Tunneling(_Tunneling):
             gas_phase (Phase): The gas phase in which the reaction occurs.
             other_properties (Dict[str, Any]): A dictionary of other properties of the tunneling reaction rate constant.
         """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.A = A if A is not None else self.A
-        self.B = B if B is not None else self.B
-        self.C = C if C is not None else self.C
-        self.reactants = (
-            [
-                (
-                    _ReactionComponent(r.name)
-                    if isinstance(r, Species)
-                    else _ReactionComponent(r[1].name, r[0])
-                )
-                for r in reactants
-            ]
-            if reactants is not None
-            else self.reactants
-        )
-        self.products = (
-            [
-                (
-                    _ReactionComponent(p.name)
-                    if isinstance(p, Species)
-                    else _ReactionComponent(p[1].name, p[0])
-                )
-                for p in products
-            ]
-            if products is not None
-            else self.products
-        )
-        self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
+        # Create the internal C++ instance
+        self._instance = _Tunneling()
 
-    @staticmethod
-    def serialize(instance) -> Dict:
+        # Set all parameters
+        if name is not None:
+            self.name = name
+        if A is not None:
+            self.A = A
+        if B is not None:
+            self.B = B
+        if C is not None:
+            self.C = C
+        if reactants is not None:
+            self.reactants = reactants
+        if products is not None:
+            self.products = products
+        if gas_phase is not None:
+            self.gas_phase = gas_phase
+        if other_properties is not None:
+            self.other_properties = other_properties
+
+    # Property delegation to self._instance
+    @property
+    def name(self) -> str:
+        """Get the name of the tunneling reaction rate constant."""
+        return self._instance.name
+
+    @name.setter
+    def name(self, value: str):
+        """Set the name of the tunneling reaction rate constant."""
+        self._instance.name = value
+
+    @property
+    def A(self) -> float:
+        """Get the pre-exponential factor."""
+        return self._instance.A
+
+    @A.setter
+    def A(self, value: float):
+        """Set the pre-exponential factor."""
+        self._instance.A = value
+
+    @property
+    def B(self) -> float:
+        """Get the tunneling parameter B."""
+        return self._instance.B
+
+    @B.setter
+    def B(self, value: float):
+        """Set the tunneling parameter B."""
+        self._instance.B = value
+
+    @property
+    def C(self) -> float:
+        """Get the tunneling parameter C."""
+        return self._instance.C
+
+    @C.setter
+    def C(self, value: float):
+        """Set the tunneling parameter C."""
+        self._instance.C = value
+
+    @property
+    def reactants(self) -> List[Union[Species, Tuple[float, Species]]]:
+        """Get the reactants as Python objects."""
+        # Convert from C++ _ReactionComponent objects to Python Species objects
+        result = []
+        for rc in self._instance.reactants:
+            if hasattr(rc, 'coefficient') and rc.coefficient != 1.0:
+                # Create a tuple with coefficient and species
+                species = Species(name=rc.species_name)
+                result.append((rc.coefficient, species))
+            else:
+                # Just the species
+                species = Species(name=rc.species_name)
+                result.append(species)
+        return result
+
+    @reactants.setter
+    def reactants(self, value: List[Union[Species, Tuple[float, Species]]]):
+        """Set the reactants, converting from Python to C++ objects."""
+        cpp_reactants = []
+        for r in value:
+            if isinstance(r, Species):
+                cpp_reactants.append(_ReactionComponent(r.name))
+            elif isinstance(r, tuple) and len(r) == 2:
+                coefficient, species = r
+                cpp_reactants.append(_ReactionComponent(species.name, coefficient))
+            else:
+                raise ValueError(f"Invalid reactant format: {r}")
+        self._instance.reactants = cpp_reactants
+
+    @property
+    def products(self) -> List[Union[Species, Tuple[float, Species]]]:
+        """Get the products as Python objects."""
+        # Convert from C++ _ReactionComponent objects to Python Species objects
+        result = []
+        for rc in self._instance.products:
+            if hasattr(rc, 'coefficient') and rc.coefficient != 1.0:
+                # Create a tuple with coefficient and species
+                species = Species(name=rc.species_name)
+                result.append((rc.coefficient, species))
+            else:
+                # Just the species
+                species = Species(name=rc.species_name)
+                result.append(species)
+        return result
+
+    @products.setter
+    def products(self, value: List[Union[Species, Tuple[float, Species]]]):
+        """Set the products, converting from Python to C++ objects."""
+        cpp_products = []
+        for p in value:
+            if isinstance(p, Species):
+                cpp_products.append(_ReactionComponent(p.name))
+            elif isinstance(p, tuple) and len(p) == 2:
+                coefficient, species = p
+                cpp_products.append(_ReactionComponent(species.name, coefficient))
+            else:
+                raise ValueError(f"Invalid product format: {p}")
+        self._instance.products = cpp_products
+
+    @property
+    def gas_phase(self) -> str:
+        """Get the gas phase name."""
+        return self._instance.gas_phase
+
+    @gas_phase.setter
+    def gas_phase(self, value: Union[Phase, str]):
+        """Set the gas phase."""
+        if isinstance(value, Phase):
+            self._instance.gas_phase = value.name
+        elif isinstance(value, str):
+            self._instance.gas_phase = value
+        else:
+            raise ValueError(f"Invalid gas_phase type: {type(value)}")
+
+    @property
+    def other_properties(self) -> Dict[str, Any]:
+        """Get the other properties."""
+        return self._instance.other_properties
+
+    @other_properties.setter
+    def other_properties(self, value: Dict[str, Any]):
+        """Set the other properties."""
+        self._instance.other_properties = value
+
+    @property
+    def type(self):
+        """Get the reaction type."""
+        return ReactionType.Tunneling
+
+    def serialize(self) -> Dict:
+        """
+        Serialize the Tunneling object to a dictionary using only Python-visible data.
+
+        Returns:
+            Dict: A dictionary representation of the Tunneling object.
+        """
         serialize_dict = {
             "type": "TUNNELING",
-            "name": instance.name,
-            "A": instance.A,
-            "B": instance.B,
-            "C": instance.C,
-            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
-            "products": ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
-            "gas phase": instance.gas_phase,
+            "name": self._instance.name,
+            "A": self._instance.A,
+            "B": self._instance.B,
+            "C": self._instance.C,
+            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(self._instance.reactants),
+            "products": ReactionComponentSerializer.serialize_list_reaction_components(self._instance.products),
+            "gas phase": self._instance.gas_phase,
         }
-        _add_other_properties(serialize_dict, instance.other_properties)
-        return _remove_empty_keys(serialize_dict)
+        _add_other_properties(serialize_dict, self.other_properties)
+        return serialize_dict
+
+    @staticmethod
+    def serialize_static(instance) -> Dict:
+        """
+        Static serialize method for compatibility with C++ _Tunneling objects.
+
+        Args:
+            instance: The _Tunneling instance to serialize.
+
+        Returns:
+            Dict: A dictionary representation of the Tunneling object.
+        """
+        # Create a temporary Tunneling object and use its serialize method
+        temp_tunneling = Tunneling()
+        temp_tunneling._instance = instance
+        return temp_tunneling.serialize()

musica/mechanism_configuration/user_defined.py

@@ -1,9 +1,13 @@
 from typing import Optional, Any, Dict, List, Union, Tuple
-from musica import _UserDefined, _ReactionComponent
+from .. import backend
 from .phase import Phase
 from .species import Species
 from .reactions import ReactionComponentSerializer
-from .utils import _add_other_properties, _remove_empty_keys
+from .utils import _add_other_properties
+
+_backend = backend.get_backend()
+_UserDefined = _backend._mechanism_configuration._UserDefined
+_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
 
 
 class UserDefined(_UserDefined):
@@ -23,7 +27,8 @@ class UserDefined(_UserDefined):
         self,
         name: Optional[str] = None,
         scaling_factor: Optional[float] = None,
-        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        reactants: Optional[List[Union[Species,
+                                       Tuple[float, Species]]]] = None,
         products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
         gas_phase: Optional[Phase] = None,
         other_properties: Optional[Dict[str, Any]] = None,
@@ -80,4 +85,4 @@ class UserDefined(_UserDefined):
             "gas phase": instance.gas_phase,
         }
         _add_other_properties(serialize_dict, instance.other_properties)
-        return _remove_empty_keys(serialize_dict)
+        return serialize_dict

musica/mechanism_configuration/wet_deposition.py

@@ -1,7 +1,10 @@
 from typing import Optional, Any, Dict
-from musica import _WetDeposition
+from .. import backend
 from .phase import Phase
-from .utils import _add_other_properties, _remove_empty_keys
+from .utils import _add_other_properties
+
+_backend = backend.get_backend()
+_WetDeposition = _backend._mechanism_configuration._WetDeposition
 
 
 class WetDeposition(_WetDeposition):
@@ -11,7 +14,7 @@ class WetDeposition(_WetDeposition):
     Attributes:
         name (str): The name of the wet deposition reaction rate constant.
         scaling_factor (float): The scaling factor for the wet deposition rate constant.
-        aerosol_phase (Phase): The aerosol phase which undergoes wet deposition.
+        condensed_phase (Phase): The condensed phase which undergoes wet deposition.
         unknown_properties (Dict[str, Any]): A dictionary of other properties of the wet deposition reaction rate constant.
     """
 
@@ -19,7 +22,7 @@ class WetDeposition(_WetDeposition):
         self,
         name: Optional[str] = None,
         scaling_factor: Optional[float] = None,
-        aerosol_phase: Optional[Phase] = None,
+        condensed_phase: Optional[Phase] = None,
         other_properties: Optional[Dict[str, Any]] = None,
     ):
         """
@@ -28,13 +31,13 @@ class WetDeposition(_WetDeposition):
         Args:
             name (str): The name of the wet deposition reaction rate constant.
             scaling_factor (float): The scaling factor for the wet deposition rate constant.
-            aerosol_phase (Phase): The aerosol phase which undergoes wet deposition.
+            condensed_phase (Phase): The condensed phase which undergoes wet deposition.
             other_properties (Dict[str, Any]): A dictionary of other properties of the wet deposition reaction rate constant.
         """
         super().__init__()
         self.name = name if name is not None else self.name
         self.scaling_factor = scaling_factor if scaling_factor is not None else self.scaling_factor
-        self.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
+        self.condensed_phase = condensed_phase.name if condensed_phase is not None else self.condensed_phase
         self.other_properties = other_properties if other_properties is not None else self.other_properties
 
     @staticmethod
@@ -43,7 +46,7 @@ class WetDeposition(_WetDeposition):
             "type": "WET_DEPOSITION",
             "name": instance.name,
             "scaling factor": instance.scaling_factor,
-            "aerosol phase": instance.aerosol_phase,
+            "condensed phase": instance.condensed_phase,
         }
         _add_other_properties(serialize_dict, instance.other_properties)
-        return _remove_empty_keys(serialize_dict)
+        return serialize_dict