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

musica/mechanism_configuration/tunneling.py

@@ -1,31 +1,38 @@
-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()
-_Tunneling = _backend._mechanism_configuration._Tunneling
-_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
-ReactionType = _backend._mechanism_configuration._ReactionType
+Tunneling = _backend._mechanism_configuration._Tunneling
 
+original_init = Tunneling.__init__
 
-class Tunneling:
-    """
-    A class representing a quantum tunneling reaction rate constant.
 
-    k = A * exp( -B / T ) * exp( C / T^3 )
+@property
+def type(self):
+    return ReactionType.Tunneling
+
 
-    where:
-        k = rate constant
-        A = pre-exponential factor [(mol m-3)^(n-1)s-1]
-        B = tunneling parameter [K^-1]
-        C = tunneling parameter [K^-3]
-        T = temperature [K]
-        n = number of reactants
+def __init__(
+    self,
+    name: Optional[str] = None,
+    A: Optional[float] = None,
+    B: Optional[float] = None,
+    C: Optional[float] = 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,
+):
+    """
+    Initializes the Tunneling object with the given parameters.
 
-    Attributes:
+    Args:
         name (str): The name of the tunneling reaction rate constant.
         A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
         B (float): Tunneling parameter [K^-1].
@@ -35,216 +42,85 @@ class 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.
     """
+    original_init(self)
+
+    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.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.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
+    )
+
+
+def serialize(self) -> Dict:
+    """
+    Serialize the Tunneling object to a dictionary using only Python-visible data.
 
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        A: Optional[float] = None,
-        B: Optional[float] = None,
-        C: Optional[float] = 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,
-    ):
-        """
-        Initializes the Tunneling object with the given parameters.
-
-        Args:
-            name (str): The name of the tunneling reaction rate constant.
-            A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
-            B (float): Tunneling parameter [K^-1].
-            C (float): Tunneling parameter [K^-3].
-            reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
-            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 tunneling reaction rate constant.
-        """
-        # Create the internal C++ instance
-        self._instance = _Tunneling()
-
-        # 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": 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, 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()
+    Returns:
+        Dict: A dictionary representation of the Tunneling object.
+    """
+    serialize_dict = {
+        "type": "TUNNELING",
+        "name": self.name,
+        "A": self.A,
+        "B": self.B,
+        "C": self.C,
+        "reactants": [r.serialize() for r in self.reactants],
+        "products": [r.serialize() for r in self.products],
+        "gas phase": self.gas_phase,
+    }
+    _add_other_properties(serialize_dict, self.other_properties)
+    return _remove_empty_keys(serialize_dict)
+
+
+Tunneling.__doc__ = """
+A class representing a quantum tunneling reaction rate constant.
+
+k = A * exp( -B / T ) * exp( C / T^3 )
+
+where:
+    k = rate constant
+    A = pre-exponential factor [(mol m-3)^(n-1)s-1]
+    B = tunneling parameter [K^-1]
+    C = tunneling parameter [K^-3]
+    T = temperature [K]
+    n = number of reactants
+
+Attributes:
+    name (str): The name of the tunneling reaction rate constant.
+    A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
+    B (float): Tunneling parameter [K^-1].
+    C (float): Tunneling parameter [K^-3].
+    reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
+    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 tunneling reaction rate constant.
+"""
+
+Tunneling.__init__ = __init__
+Tunneling.serialize = serialize
+Tunneling.type = type

musica/mechanism_configuration/user_defined.py

@@ -2,19 +2,35 @@ from typing import Optional, Any, Dict, List, Union, Tuple
 from .. import backend
 from .phase import Phase
 from .species import Species
-from .reactions import ReactionComponentSerializer
-from .utils import _add_other_properties
+from .utils import _add_other_properties, _remove_empty_keys
+from .reaction_component import ReactionComponent
+from .ancillary import ReactionType
 
 _backend = backend.get_backend()
-_UserDefined = _backend._mechanism_configuration._UserDefined
-_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
+UserDefined = _backend._mechanism_configuration._UserDefined
 
+original_init = UserDefined.__init__
 
-class UserDefined(_UserDefined):
+
+@property
+def type(self):
+    return ReactionType.UserDefined
+
+
+def __init__(
+    self,
+    name: Optional[str] = None,
+    scaling_factor: Optional[float] = 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,
+):
     """
-    A class representing a user-defined reaction rate constant.
+    Initializes the UserDefined object with the given parameters.
 
-    Attributes:
+    Args:
         name (str): The name of the photolysis reaction rate constant.
         scaling_factor (float): The scaling factor for the photolysis rate constant.
         reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
@@ -22,67 +38,62 @@ class UserDefined(_UserDefined):
         gas_phase (Phase): The gas phase in which the reaction occurs.
         other_properties (Dict[str, Any]): A dictionary of other properties of the photolysis 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.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
+
+
+def serialize(self) -> Dict:
+    serialize_dict = {
+        "type": "USER_DEFINED",
+        "name": self.name,
+        "scaling factor": self.scaling_factor,
+        "reactants": [r.serialize() for r in self.reactants],
+        "products": [r.serialize() for r in self.products],
+        "gas phase": self.gas_phase,
+    }
+    _add_other_properties(serialize_dict, self.other_properties)
+    return _remove_empty_keys(serialize_dict)
+
 
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        scaling_factor: Optional[float] = 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,
-    ):
-        """
-        Initializes the UserDefined object with the given parameters.
+UserDefined.__doc__ = """
+A class representing a user-defined reaction rate constant.
 
-        Args:
-            name (str): The name of the photolysis reaction rate constant.
-            scaling_factor (float): The scaling factor for the photolysis rate constant.
-            reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
-            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 photolysis 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.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
+Attributes:
+    name (str): The name of the photolysis reaction rate constant.
+    scaling_factor (float): The scaling factor for the photolysis rate constant.
+    reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
+    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 photolysis reaction rate constant.
+"""
 
-    @staticmethod
-    def serialize(instance) -> Dict:
-        serialize_dict = {
-            "type": "USER_DEFINED",
-            "name": instance.name,
-            "scaling factor": instance.scaling_factor,
-            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
-            "products": ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
-            "gas phase": instance.gas_phase,
-        }
-        _add_other_properties(serialize_dict, instance.other_properties)
-        return serialize_dict
+UserDefined.__init__ = __init__
+UserDefined.serialize = serialize
+UserDefined.type = type