musica 0.12.0__cp312-cp312-win_amd64.whl → 0.12.2__cp312-cp312-win_amd64.whl

musica/mechanism_configuration/arrhenius.py

@@ -1,13 +1,18 @@
 from typing import Optional, Any, Dict, List, Union, Tuple
-from musica import _Arrhenius, _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 musica.constants import BOLTZMANN
+from .utils import _add_other_properties
+from ..constants import BOLTZMANN
 
+_backend = backend.get_backend()
+_Arrhenius = _backend._mechanism_configuration._Arrhenius
+_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
+ReactionType = _backend._mechanism_configuration._ReactionType
 
-class Arrhenius(_Arrhenius):
+
+class Arrhenius:
     """
     A class representing an Arrhenius rate constant.
 
@@ -46,7 +51,8 @@ class Arrhenius(_Arrhenius):
         Ea: Optional[float] = None,
         D: Optional[float] = None,
         E: 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,
@@ -67,45 +73,199 @@ class Arrhenius(_Arrhenius):
             gas_phase (Phase): The gas phase in which the reaction occurs.
             other_properties (Dict[str, Any]): A dictionary of other properties of the Arrhenius 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
+        # Create the internal C++ instance
+        self._instance = _Arrhenius()
+
+        # Validate mutually exclusive parameters
         if C is not None and Ea is not None:
             raise ValueError("Cannot specify both C and Ea.")
-        self.C = -Ea / BOLTZMANN if Ea is not None else C if C is not None else self.C
-        self.D = D if D is not None else self.D
-        self.E = E if E is not None else self.E
-        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
 
-    @staticmethod
-    def serialize(instance) -> Dict:
-        serialize_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 Ea is not None:
+            self.C = -Ea / BOLTZMANN
+        elif C is not None:
+            self.C = C
+        if D is not None:
+            self.D = D
+        if E is not None:
+            self.E = E
+        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 Arrhenius rate constant."""
+        return self._instance.name
+
+    @name.setter
+    def name(self, value: str):
+        """Set the name of the Arrhenius 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 temperature exponent."""
+        return self._instance.B
+
+    @B.setter
+    def B(self, value: float):
+        """Set the temperature exponent."""
+        self._instance.B = value
+
+    @property
+    def C(self) -> float:
+        """Get the exponential term."""
+        return self._instance.C
+
+    @C.setter
+    def C(self, value: float):
+        """Set the exponential term."""
+        self._instance.C = value
+
+    @property
+    def D(self) -> float:
+        """Get the reference temperature."""
+        return self._instance.D
+
+    @D.setter
+    def D(self, value: float):
+        """Set the reference temperature."""
+        self._instance.D = value
+
+    @property
+    def E(self) -> float:
+        """Get the pressure scaling term."""
+        return self._instance.E
+
+    @E.setter
+    def E(self, value: float):
+        """Set the pressure scaling term."""
+        self._instance.E = 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.Arrhenius
+
+    def _create_serialize_dict(self, instance) -> Dict:
+        """
+        Helper method to create the serialization dictionary.
+
+        Args:
+            instance: The instance to serialize (either self._instance or a _Arrhenius object).
+
+        Returns:
+            Dict: Base serialization dictionary.
+        """
+        return {
             "type": "ARRHENIUS",
             "name": instance.name,
             "A": instance.A,
@@ -117,5 +277,31 @@ class Arrhenius(_Arrhenius):
             "products": ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
             "gas phase": instance.gas_phase,
         }
+
+    def serialize(self) -> Dict:
+        """
+        Serialize the Arrhenius object to a dictionary using only Python-visible data.
+
+        Returns:
+            Dict: A dictionary representation of the Arrhenius object.
+        """
+        serialize_dict = self._create_serialize_dict(self._instance)
+        _add_other_properties(serialize_dict, self.other_properties)
+        return serialize_dict
+
+    @staticmethod
+    def serialize_static(instance) -> Dict:
+        """
+        Static serialize method for compatibility with C++ _Arrhenius objects.
+
+        Args:
+            instance: The _Arrhenius instance to serialize.
+
+        Returns:
+            Dict: A dictionary representation of the Arrhenius object.
+        """
+        # Create a temporary Arrhenius object to use the helper method
+        temp_arrhenius = Arrhenius()
+        serialize_dict = temp_arrhenius._create_serialize_dict(instance)
         _add_other_properties(serialize_dict, instance.other_properties)
-        return _remove_empty_keys(serialize_dict)
+        return serialize_dict

musica/mechanism_configuration/branched.py

@@ -1,12 +1,17 @@
-from typing import Optional, Any, Dict, List, Union, Tuple
-from musica import _Branched, _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()
+_Branched = _backend._mechanism_configuration._Branched
+_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
+ReactionType = _backend._mechanism_configuration._ReactionType
 
 
-class Branched(_Branched):
+class Branched:
     """
     A class representing a branched reaction rate constant.
 
@@ -32,9 +37,12 @@ class Branched(_Branched):
         Y: Optional[float] = None,
         a0: Optional[float] = None,
         n: Optional[float] = None,
-        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        nitrate_products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        alkoxy_products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        reactants: Optional[List[Union[Species,
+                                       Tuple[float, Species]]]] = None,
+        nitrate_products: Optional[List[Union[Species,
+                                              Tuple[float, Species]]]] = None,
+        alkoxy_products: Optional[List[Union[Species,
+                                             Tuple[float, Species]]]] = None,
         gas_phase: Optional[Phase] = None,
         other_properties: Optional[Dict[str, Any]] = None,
     ):
@@ -53,64 +61,239 @@ class Branched(_Branched):
             gas_phase (Phase): The gas phase in which the reaction occurs.
             other_properties (Dict[str, Any]): A dictionary of other properties of the branched reaction rate constant.
         """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.X = X if X is not None else self.X
-        self.Y = Y if Y is not None else self.Y
-        self.a0 = a0 if a0 is not None else self.a0
-        self.n = n if n is not None else self.n
-        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.nitrate_products = (
-            [
-                (
-                    _ReactionComponent(p.name)
-                    if isinstance(p, Species)
-                    else _ReactionComponent(p[1].name, p[0])
-                )
-                for p in nitrate_products
-            ]
-            if nitrate_products is not None
-            else self.nitrate_products
-        )
-        self.alkoxy_products = (
-            [
-                (
-                    _ReactionComponent(p.name)
-                    if isinstance(p, Species)
-                    else _ReactionComponent(p[1].name, p[0])
-                )
-                for p in alkoxy_products
-            ]
-            if alkoxy_products is not None
-            else self.alkoxy_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 = _Branched()
 
-    @staticmethod
-    def serialize(instance) -> Dict:
+        # Set all parameters
+        if name is not None:
+            self.name = name
+        if X is not None:
+            self.X = X
+        if Y is not None:
+            self.Y = Y
+        if a0 is not None:
+            self.a0 = a0
+        if n is not None:
+            self.n = n
+        if reactants is not None:
+            self.reactants = reactants
+        if nitrate_products is not None:
+            self.nitrate_products = nitrate_products
+        if alkoxy_products is not None:
+            self.alkoxy_products = alkoxy_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 branched reaction rate constant."""
+        return self._instance.name
+
+    @name.setter
+    def name(self, value: str):
+        """Set the name of the branched reaction rate constant."""
+        self._instance.name = value
+
+    @property
+    def X(self) -> float:
+        """Get the pre-exponential branching factor."""
+        return self._instance.X
+
+    @X.setter
+    def X(self, value: float):
+        """Set the pre-exponential branching factor."""
+        self._instance.X = value
+
+    @property
+    def Y(self) -> float:
+        """Get the exponential branching factor."""
+        return self._instance.Y
+
+    @Y.setter
+    def Y(self, value: float):
+        """Set the exponential branching factor."""
+        self._instance.Y = value
+
+    @property
+    def a0(self) -> float:
+        """Get the Z parameter."""
+        return self._instance.a0
+
+    @a0.setter
+    def a0(self, value: float):
+        """Set the Z parameter."""
+        self._instance.a0 = value
+
+    @property
+    def n(self) -> float:
+        """Get the A parameter."""
+        return self._instance.n
+
+    @n.setter
+    def n(self, value: float):
+        """Set the A parameter."""
+        self._instance.n = 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 nitrate_products(self) -> List[Union[Species, Tuple[float, Species]]]:
+        """Get the nitrate products as Python objects."""
+        # Convert from C++ _ReactionComponent objects to Python Species objects
+        result = []
+        for rc in self._instance.nitrate_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
+
+    @nitrate_products.setter
+    def nitrate_products(self, value: List[Union[Species, Tuple[float, Species]]]):
+        """Set the nitrate 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 nitrate product format: {p}")
+        self._instance.nitrate_products = cpp_products
+
+    @property
+    def alkoxy_products(self) -> List[Union[Species, Tuple[float, Species]]]:
+        """Get the alkoxy products as Python objects."""
+        # Convert from C++ _ReactionComponent objects to Python Species objects
+        result = []
+        for rc in self._instance.alkoxy_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
+
+    @alkoxy_products.setter
+    def alkoxy_products(self, value: List[Union[Species, Tuple[float, Species]]]):
+        """Set the alkoxy 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 alkoxy product format: {p}")
+        self._instance.alkoxy_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.Branched
+
+    def serialize(self) -> Dict:
+        """
+        Serialize the Branched object to a dictionary using only Python-visible data.
+
+        Returns:
+            Dict: A dictionary representation of the Branched object.
+        """
         serialize_dict = {
             "type": "BRANCHED_NO_RO2",
-            "name": instance.name,
-            "X": instance.X,
-            "Y": instance.Y,
-            "a0": instance.a0,
-            "n": instance.n,
-            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
-            "nitrate products": ReactionComponentSerializer.serialize_list_reaction_components(instance.nitrate_products),
-            "alkoxy products": ReactionComponentSerializer.serialize_list_reaction_components(instance.alkoxy_products),
-            "gas phase": instance.gas_phase,
+            "name": self.name,
+            "X": self.X,
+            "Y": self.Y,
+            "a0": self.a0,
+            "n": self.n,
+            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(
+                self._instance.reactants),
+            "nitrate products": ReactionComponentSerializer.serialize_list_reaction_components(
+                self._instance.nitrate_products),
+            "alkoxy products": ReactionComponentSerializer.serialize_list_reaction_components(
+                self._instance.alkoxy_products),
+            "gas phase": self.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++ _Branched objects.
+
+        Args:
+            instance: The _Branched instance to serialize.
+
+        Returns:
+            Dict: A dictionary representation of the Branched object.
+        """
+        # Create a temporary Branched object and use its instance serialize method
+        temp_branched = Branched()
+        temp_branched._instance = instance
+        return temp_branched.serialize()