musica 0.12.2__cp39-cp39-macosx_15_0_arm64.whl → 0.13.0__cp39-cp39-macosx_15_0_arm64.whl

musica/mechanism_configuration/branched.py

@@ -1,22 +1,127 @@
-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
+from .reaction_component import ReactionComponent
+from .ancillary import ReactionType
 
 _backend = backend.get_backend()
-_Branched = _backend._mechanism_configuration._Branched
-_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
-ReactionType = _backend._mechanism_configuration._ReactionType
+Branched = _backend._mechanism_configuration._Branched
+
+original_init = Branched.__init__
+
+
+@property
+def type(self):
+    """Get the reaction type."""
+    return ReactionType.Branched
+
+
+def __init__(
+    self,
+    name: Optional[str] = None,
+    X: Optional[float] = None,
+    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,
+    gas_phase: Optional[Phase] = None,
+    other_properties: Optional[Dict[str, Any]] = None,
+):
+    """
+    Initializes the Branched object with the given parameters.
 
+    Args:
+        name (str): The name of the branched reaction rate constant.
+        X (float): Pre-exponential branching factor [(mol m-3)^-(n-1)s-1].
+        Y (float): Exponential branching factor [K-1].
+        a0 (float): Z parameter [unitless].
+        n (float): A parameter [unitless].
+        reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
+        nitrate_products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the nitrate branch.
+        alkoxy_products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the alkoxy branch.
+        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.
+    """
+    original_init(self)
+
+    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.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
+    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
+    )
+
+
+def serialize(self) -> Dict:
+    """
+    Serialize the Branched object to a dictionary using only Python-visible data.
 
-class Branched:
+    Returns:
+        Dict: A dictionary representation of the Branched object.
     """
+    serialize_dict = {
+        "type": "BRANCHED_NO_RO2",
+        "name": self.name,
+        "X": self.X,
+        "Y": self.Y,
+        "a0": self.a0,
+        "n": self.n,
+        "reactants": [r.serialize() for r in self.reactants],
+        "nitrate products": [r.serialize() for r in self.nitrate_products],
+        "alkoxy products": [r.serialize() for r in self.alkoxy_products],
+        "gas phase": self.gas_phase,
+    }
+    _add_other_properties(serialize_dict, self.other_properties)
+    return _remove_empty_keys(serialize_dict)
+
+
+Branched.__doc__ = """
     A class representing a branched reaction rate constant.
 
-    (TODO: get details from MusicBox)
-
     Attributes:
         name (str): The name of the branched reaction rate constant.
         X (float): Pre-exponential branching factor [(mol m-3)^-(n-1)s-1].
@@ -30,270 +135,6 @@ class Branched:
         other_properties (Dict[str, Any]): A dictionary of other properties of the branched reaction rate constant.
     """
 
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        X: Optional[float] = None,
-        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,
-        gas_phase: Optional[Phase] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the Branched object with the given parameters.
-
-        Args:
-            name (str): The name of the branched reaction rate constant.
-            X (float): Pre-exponential branching factor [(mol m-3)^-(n-1)s-1].
-            Y (float): Exponential branching factor [K-1].
-            a0 (float): Z parameter [unitless].
-            n (float): A parameter [unitless].
-            reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
-            nitrate_products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the nitrate branch.
-            alkoxy_products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the alkoxy branch.
-            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.
-        """
-        # Create the internal C++ instance
-        self._instance = _Branched()
-
-        # 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": 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, 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()
+Branched.__init__ = __init__
+Branched.serialize = serialize
+Branched.type = type

musica/mechanism_configuration/emission.py

@@ -1,71 +1,82 @@
-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
+from .reaction_component import ReactionComponent
+from .ancillary import ReactionType
 
 _backend = backend.get_backend()
-_Emission = _backend._mechanism_configuration._Emission
-_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
+Emission = _backend._mechanism_configuration._Emission
 
+original_init = Emission.__init__
 
-class Emission(_Emission):
+
+@property
+def type(self):
+    return ReactionType.Emission
+
+
+def __init__(
+    self,
+    name: Optional[str] = None,
+    scaling_factor: Optional[float] = None,
+    products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+    gas_phase: Optional[Phase] = None,
+    other_properties: Optional[Dict[str, Any]] = None,
+):
     """
-    A class representing an emission reaction rate constant.
+    Initializes the Emission object with the given parameters.
 
-    Attributes:
+    Args:
         name (str): The name of the emission reaction rate constant.
         scaling_factor (float): The scaling factor for the emission rate constant.
         products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
         gas_phase (Phase): The gas phase in which the reaction occurs.
         other_properties (Dict[str, Any]): A dictionary of other properties of the emission reaction rate constant.
     """
+    original_init(self)
+    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.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
+
+
+def serialize(self) -> Dict:
+    serialize_dict = {
+        "type": "EMISSION",
+        "name": self.name,
+        "scaling factor": self.scaling_factor,
+        "products": [r.serialize() for r in self.products],
+        "gas phase": self.gas_phase,
+    }
+    _add_other_properties(serialize_dict, self.other_properties)
+    return serialize_dict
+
 
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        scaling_factor: Optional[float] = None,
-        products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        gas_phase: Optional[Phase] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the Emission object with the given parameters.
+Emission.__doc__ = """
+A class representing an emission reaction rate constant.
 
-        Args:
-            name (str): The name of the emission reaction rate constant.
-            scaling_factor (float): The scaling factor for the emission rate constant.
-            products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
-            gas_phase (Phase): The gas phase in which the reaction occurs.
-            other_properties (Dict[str, Any]): A dictionary of other properties of the emission 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.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
+Attributes:
+    name (str): The name of the emission reaction rate constant.
+    scaling_factor (float): The scaling factor for the emission rate constant.
+    products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
+    gas_phase (Phase): The gas phase in which the reaction occurs.
+    other_properties (Dict[str, Any]): A dictionary of other properties of the emission reaction rate constant.
+"""
 
-    @staticmethod
-    def serialize(instance) -> Dict:
-        serialize_dict = {
-            "type": "EMISSION",
-            "name": instance.name,
-            "scaling factor": instance.scaling_factor,
-            "products": ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
-            "gas phase": instance.gas_phase,
-        }
-        _add_other_properties(serialize_dict, instance.other_properties)
-        return serialize_dict
+Emission.__init__ = __init__
+Emission.serialize = serialize
+Emission.type = type