musica 0.11.1.1__cp312-cp312-win_amd64.whl → 0.14.2__cp312-cp312-win_amd64.whl

musica/mechanism_configuration.py

@@ -1,1291 +0,0 @@
-# Copyright (C) 2025 University Corporation for Atmospheric Research
-# SPDX-License-Identifier: Apache-2.0
-#
-# This file is part of the musica Python package.
-# For more information, see the LICENSE file in the top-level directory of this distribution.
-from typing import Optional, Any, Dict, List, Union, Tuple
-from _musica._mechanism_configuration import (
-    _ReactionType,
-    _Species,
-    _Phase,
-    _ReactionComponent,
-    _Arrhenius,
-    _CondensedPhaseArrhenius,
-    _Troe,
-    _Branched,
-    _Tunneling,
-    _Surface,
-    _Photolysis,
-    _CondensedPhasePhotolysis,
-    _Emission,
-    _FirstOrderLoss,
-    _AqueousEquilibrium,
-    _WetDeposition,
-    _HenrysLaw,
-    _SimpolPhaseTransfer,
-    _UserDefined,
-    _Reactions,
-    _ReactionsIterator,
-    _Mechanism,
-    _Version,
-    _Parser,
-)
-
-BOLTZMANN_CONSTANT_J_K = 1.380649e-23  # J K-1
-
-
-class ReactionType(_ReactionType):
-    """
-    A enum class representing a reaction type in a chemical mechanism.
-    """
-
-
-class Species(_Species):
-    """
-    A class representing a species in a chemical mechanism.
-
-    Attributes:
-        name (str): The name of the species.
-        HLC_298K_mol_m3_Pa (float): Henry's Law Constant at 298K [mol m-3 Pa-1]
-        HLC_exponential_factor_K: Henry's Law Constant exponential factor [K]
-        diffusion_coefficient_m2_s (float): Diffusion coefficient [m2 s-1]
-        N_star (float): A parameter used to calculate the mass accomodation factor (Ervens et al., 2003)
-        molecular_weight_kg_mol (float): Molecular weight [kg mol-1]
-        density_kg_m3 (float): Density [kg m-3]
-        tracer_type (str): The type of tracer ("AEROSOL", "THIRD_BODY", "CONSTANT").
-        other_properties (Dict[str, Any]): A dictionary of other properties of the species.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        HLC_298K_mol_m3_Pa: Optional[float] = None,
-        HLC_exponential_factor_K: Optional[float] = None,
-        diffusion_coefficient_m2_s: Optional[float] = None,
-        N_star: Optional[float] = None,
-        molecular_weight_kg_mol: Optional[float] = None,
-        density_kg_m3: Optional[float] = None,
-        tracer_type: Optional[str] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the Species object with the given parameters.
-
-        Args:
-            name (str): The name of the species.
-            HLC_298K_mol_m3_Pa (float): Henry's Law Constant at 298K [mol m-3 Pa-1]
-            HLC_exponential_factor_K: Henry's Law Constant exponential factor [K]
-            diffusion_coefficient_m2_s (float): Diffusion coefficient [m2 s-1]
-            N_star (float): A parameter used to calculate the mass accomodation factor (Ervens et al., 2003)
-            molecular_weight_kg_mol (float): Molecular weight [kg mol-1]
-            density_kg_m3 (float): Density [kg m-3]
-            tracer_type (str): The type of tracer ("AEROSOL", "THIRD_BODY", "CONSTANT").
-            other_properties (Dict[str, Any]): A dictionary of other properties of the species.
-        """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.HLC_298K_mol_m3_Pa = HLC_298K_mol_m3_Pa if HLC_298K_mol_m3_Pa is not None else self.HLC_298K_mol_m3_Pa
-        self.HLC_exponential_factor_K = HLC_exponential_factor_K if HLC_exponential_factor_K is not None else self.HLC_exponential_factor_K
-        self.diffusion_coefficient_m2_s = diffusion_coefficient_m2_s if diffusion_coefficient_m2_s is not None else self.diffusion_coefficient_m2_s
-        self.N_star = N_star if N_star is not None else self.N_star
-        self.molecular_weight_kg_mol = molecular_weight_kg_mol if molecular_weight_kg_mol is not None else self.molecular_weight_kg_mol
-        self.density_kg_m3 = density_kg_m3 if density_kg_m3 is not None else self.density_kg_m3
-        self.tracer_type = tracer_type if tracer_type is not None else self.tracer_type
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
-
-
-class Phase(_Phase):
-    """
-    A class representing a phase in a chemical mechanism.
-
-    Attributes:
-        name (str): The name of the phase.
-        species (List[Species]): A list of species in the phase.
-        other_properties (Dict[str, Any]): A dictionary of other properties of the phase.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        species: Optional[List[Species]] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the Phase object with the given parameters.
-
-        Args:
-            name (str): The name of the phase.
-            species (List[Species]): A list of species in the phase.
-            other_properties (Dict[str, Any]): A dictionary of other properties of the phase.
-        """
-        super().__init__()
-        self.name = name
-        self.species = [s.name for s in species] if species is not None else self.species
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
-
-
-class Arrhenius(_Arrhenius):
-    """
-    A class representing an Arrhenius rate constant.
-
-    k = A * exp( C / T ) * ( T / D )^B * exp( 1 - E * P )
-
-    where:
-        k = rate constant
-        A = pre-exponential factor [(mol m-3)^(n-1)s-1]
-        B = temperature exponent [unitless]
-        C = exponential term [K-1]
-        D = reference temperature [K]
-        E = pressure scaling term [Pa-1]
-        T = temperature [K]
-        P = pressure [Pa]
-        n = number of reactants
-
-    Attributes:
-        name (str): The name of the Arrhenius rate constant.
-        A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1] where n is the number of reactants.
-        B (float): Temperature exponent [unitless].
-        C (float): Exponential term [K-1].
-        D (float): Reference Temperature [K].
-        E (float): Pressure scaling term [Pa-1].
-        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 Arrhenius rate constant.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        A: Optional[float] = None,
-        B: Optional[float] = None,
-        C: Optional[float] = None,
-        Ea: Optional[float] = None,
-        D: Optional[float] = None,
-        E: 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 Arrhenius object with the given parameters.
-
-        Args:
-            name (str): The name of the Arrhenius rate constant.
-            A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1] where n is the number of reactants.
-            B (float): Temperature exponent [unitless].
-            C (float): Exponential term [K-1].
-            Ea (float): Activation energy [J molecule-1].
-            D (float): Reference Temperature [K].
-            E (float): Pressure scaling term [Pa-1].
-            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 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
-        if C is not None and Ea is not None:
-            raise ValueError("Cannot specify both C and Ea.")
-        self.C = -Ea / BOLTZMANN_CONSTANT_J_K 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
-
-
-class CondensedPhaseArrhenius(_CondensedPhaseArrhenius):
-    """
-    A class representing a condensed phase Arrhenius rate constant.
-
-    Attributes:
-        name (str): The name of the condensed phase Arrhenius rate constant.
-        A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
-        B (float): Temperature exponent [unitless].
-        C (float): Exponential term [K-1].
-        Ea (float): Activation energy [J molecule-1].
-        D (float): Reference Temperature [K].
-        E (float): Pressure scaling term [Pa-1].
-        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.
-        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-        aerosol_phase_water (Species): The water species in the aerosol phase.
-        other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase Arrhenius rate constant.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        A: Optional[float] = None,
-        B: Optional[float] = None,
-        C: Optional[float] = None,
-        Ea: Optional[float] = None,
-        D: Optional[float] = None,
-        E: Optional[float] = None,
-        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        aerosol_phase: Optional[Phase] = None,
-        aerosol_phase_water: Optional[Species] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the CondensedPhaseArrhenius object with the given parameters.
-
-        Args:
-            name (str): The name of the condensed phase Arrhenius rate constant.
-            A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
-            B (float): Temperature exponent [unitless].
-            C (float): Exponential term [K-1].
-            Ea (float): Activation energy [J molecule-1].
-            D (float): Reference Temperature [K].
-            E (float): Pressure scaling term [Pa-1].
-            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.
-            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-            aerosol_phase_water (Species): The water species in the aerosol phase.
-            other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase 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
-        if C is not None and Ea is not None:
-            raise ValueError("Cannot specify both C and Ea.")
-        self.C = -Ea / BOLTZMANN_CONSTANT_J_K 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.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
-        self.aerosol_phase_water = (
-            aerosol_phase_water.name if aerosol_phase_water is not None else self.aerosol_phase_water
-        )
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
-
-
-class Troe(_Troe):
-    """
-    A class representing a Troe rate constant.
-
-    Attributes:
-        name (str): The name of the Troe rate constant.
-        k0_A (float): Pre-exponential factor for the low-pressure limit [(mol m-3)^(n-1)s-1].
-        k0_B (float): Temperature exponent for the low-pressure limit [unitless].
-        k0_C (float): Exponential term for the low-pressure limit [K-1].
-        kinf_A (float): Pre-exponential factor for the high-pressure limit [(mol m-3)^(n-1)s-1].
-        kinf_B (float): Temperature exponent for the high-pressure limit [unitless].
-        kinf_C (float): Exponential term for the high-pressure limit [K-1].
-        Fc (float): Troe parameter [unitless].
-        N (float): Troe parameter [unitless].
-        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 Troe rate constant.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        k0_A: Optional[float] = None,
-        k0_B: Optional[float] = None,
-        k0_C: Optional[float] = None,
-        kinf_A: Optional[float] = None,
-        kinf_B: Optional[float] = None,
-        kinf_C: Optional[float] = None,
-        Fc: Optional[float] = None,
-        N: 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 Troe object with the given parameters.
-
-        k0 = k0_A * exp( k0_C / T ) * ( T / 300.0 )^k0_B
-        kinf = kinf_A * exp( kinf_C / T ) * ( T / 300.0 )^kinf_B
-        k = k0[M] / ( 1 + k0[M] / kinf ) * Fc^(1 + 1/N*(log10(k0[M]/kinf))^2)^-1
-
-        where:
-            k = rate constant
-            k0 = low-pressure limit rate constant
-            kinf = high-pressure limit rate constant
-            k0_A = pre-exponential factor for the low-pressure limit [(mol m-3)^(n-1)s-1]
-            k0_B = temperature exponent for the low-pressure limit [unitless]
-            k0_C = exponential term for the low-pressure limit [K-1]
-            kinf_A = pre-exponential factor for the high-pressure limit [(mol m-3)^(n-1)s-1]
-            kinf_B = temperature exponent for the high-pressure limit [unitless]
-            kinf_C = exponential term for the high-pressure limit [K-1]
-            Fc = Troe parameter [unitless]
-            N = Troe parameter [unitless]
-            T = temperature [K]
-            M = concentration of the third body [mol m-3]
-
-        Args:
-            name (str): The name of the Troe rate constant.
-            k0_A (float): Pre-exponential factor for the low-pressure limit [(mol m-3)^(n-1)s-1].
-            k0_B (float): Temperature exponent for the low-pressure limit [unitless].
-            k0_C (float): Exponential term for the low-pressure limit [K-1].
-            kinf_A (float): Pre-exponential factor for the high-pressure limit [(mol m-3)^(n-1)s-1].
-            kinf_B (float): Temperature exponent for the high-pressure limit [unitless].
-            kinf_C (float): Exponential term for the high-pressure limit [K-1].
-            Fc (float): Troe parameter [unitless].
-            N (float): Troe parameter [unitless].
-            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 Troe rate constant.
-        """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.k0_A = k0_A if k0_A is not None else self.k0_A
-        self.k0_B = k0_B if k0_B is not None else self.k0_B
-        self.k0_C = k0_C if k0_C is not None else self.k0_C
-        self.kinf_A = kinf_A if kinf_A is not None else self.kinf_A
-        self.kinf_B = kinf_B if kinf_B is not None else self.kinf_B
-        self.kinf_C = kinf_C if kinf_C is not None else self.kinf_C
-        self.Fc = Fc if Fc is not None else self.Fc
-        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.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
-
-
-class Branched(_Branched):
-    """
-    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].
-        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.
-    """
-
-    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.
-        """
-        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
-
-
-class Tunneling(_Tunneling):
-    """
-    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.
-    """
-
-    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.
-        """
-        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
-
-
-class Surface(_Surface):
-    """
-    A class representing a surface in a chemical mechanism.
-
-    (TODO: get details from MusicBox)
-
-    Attributes:
-        name (str): The name of the surface.
-        reaction_probability (float): The probability of a reaction occurring on the surface.
-        gas_phase_species (Union[Species, Tuple[float, Species]]): The gas phase species involved in the reaction.
-        gas_phase_products (List[Union[Species, Tuple[float, Species]]]): The gas phase products formed in the reaction.
-        gas_phase (Phase): The gas phase in which the reaction occurs.
-        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-        other_properties (Dict[str, Any]): A dictionary of other properties of the surface.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        reaction_probability: Optional[float] = None,
-        gas_phase_species: Optional[Union[Species, Tuple[float, Species]]] = None,
-        gas_phase_products: Optional[
-            List[Union[Species, Tuple[float, Species]]]
-        ] = None,
-        gas_phase: Optional[Phase] = None,
-        aerosol_phase: Optional[Phase] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the Surface object with the given parameters.
-
-        Args:
-            name (str): The name of the surface.
-            reaction_probability (float): The probability of a reaction occurring on the surface.
-            gas_phase_species (Union[Species, Tuple[float, Species]]): The gas phase species involved in the reaction.
-            gas_phase_products (List[Union[Species, Tuple[float, Species]]]): The gas phase products formed in the reaction.
-            gas_phase (Phase): The gas phase in which the reaction occurs.
-            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-            other_properties (Dict[str, Any]): A dictionary of other properties of the surface.
-        """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.reaction_probability = reaction_probability if reaction_probability is not None else self.reaction_probability
-        self.gas_phase_species = (
-            (
-                _ReactionComponent(gas_phase_species.name)
-                if isinstance(gas_phase_species, Species)
-                else _ReactionComponent(gas_phase_species[1].name, gas_phase_species[0])
-            )
-            if gas_phase_species is not None
-            else self.gas_phase_species
-        )
-        self.gas_phase_products = (
-            [
-                (
-                    _ReactionComponent(p.name)
-                    if isinstance(p, Species)
-                    else _ReactionComponent(p[1].name, p[0])
-                )
-                for p in gas_phase_products
-            ]
-            if gas_phase_products is not None
-            else self.gas_phase_products
-        )
-        self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
-        self.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
-
-
-class Photolysis(_Photolysis):
-    """
-    A class representing a photolysis reaction rate constant.
-
-    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.
-    """
-
-    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 Photolysis object with the given parameters.
-
-        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 = 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
-
-
-class CondensedPhasePhotolysis(_CondensedPhasePhotolysis):
-    """
-    A class representing a condensed phase photolysis reaction rate constant.
-
-    Attributes:
-        name (str): The name of the condensed phase 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.
-        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-        aerosol_phase_water (float): The water species in the aerosol phase [unitless].
-        other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase photolysis reaction rate constant.
-    """
-
-    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,
-        aerosol_phase: Optional[Phase] = None,
-        aerosol_phase_water: Optional[Species] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the CondensedPhasePhotolysis object with the given parameters.
-
-        Args:
-            name (str): The name of the condensed phase 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.
-            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-            aerosol_phase_water (Species): The water species in the aerosol phase [unitless].
-            other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase 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.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
-        self.aerosol_phase_water = (
-            aerosol_phase_water.name if aerosol_phase_water is not None else self.aerosol_phase_water
-        )
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
-
-
-class Emission(_Emission):
-    """
-    A class representing an emission reaction rate constant.
-
-    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.
-    """
-
-    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.
-
-        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
-
-
-class FirstOrderLoss(_FirstOrderLoss):
-    """
-    A class representing a first-order loss reaction rate constant.
-
-    Attributes:
-        name (str): The name of the first-order loss reaction rate constant.
-        scaling_factor (float): The scaling factor for the first-order loss rate constant.
-        reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved 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 first-order loss reaction rate constant.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        scaling_factor: Optional[float] = None,
-        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        gas_phase: Optional[Phase] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the FirstOrderLoss object with the given parameters.
-
-        Args:
-            name (str): The name of the first-order loss reaction rate constant.
-            scaling_factor (float): The scaling factor for the first-order loss rate constant.
-            reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved 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 first-order loss 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.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
-
-
-class AqueousEquilibrium(_AqueousEquilibrium):
-    """
-    A class representing an aqueous equilibrium reaction rate constant.
-
-    Attributes:
-        name (str): The name of the aqueous equilibrium reaction rate constant.
-        gas_phase (Phase): The gas phase in which the reaction occurs.
-        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-        aerosol_phase_water (Species): The water species in the aerosol phase.
-        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.
-        A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
-        C (float): Exponential term [K-1].
-        k_reverse (float): Reverse rate constant [(mol m-3)^(n-1)s-1].
-        other_properties (Dict[str, Any]): A dictionary of other properties of the aqueous equilibrium reaction rate constant.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        gas_phase: Optional[Phase] = None,
-        aerosol_phase: Optional[Phase] = None,
-        aerosol_phase_water: Optional[Species] = None,
-        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        A: Optional[float] = None,
-        C: Optional[float] = None,
-        k_reverse: Optional[float] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the AqueousEquilibrium object with the given parameters.
-
-        Args:
-            name (str): The name of the aqueous equilibrium reaction rate constant.
-            gas_phase (Phase): The gas phase in which the reaction occurs.
-            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-            aerosol_phase_water (Species): The water species in the aerosol phase.
-            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.
-            A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
-            C (float): Exponential term [K-1].
-            k_reverse (float): Reverse rate constant [(mol m-3)^(n-1)s-1].
-            other_properties (Dict[str, Any]): A dictionary of other properties of the aqueous equilibrium reaction rate constant.
-        """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
-        self.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
-        self.aerosol_phase_water = (
-            aerosol_phase_water.name if aerosol_phase_water is not None else self.aerosol_phase_water
-        )
-        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.A = A if A is not None else self.A
-        self.C = C if C is not None else self.C
-        self.k_reverse = k_reverse if k_reverse is not None else self.k_reverse
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
-
-
-class WetDeposition(_WetDeposition):
-    """
-    A class representing a wet deposition reaction rate constant.
-
-    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.
-        unknown_properties (Dict[str, Any]): A dictionary of other properties of the wet deposition reaction rate constant.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        scaling_factor: Optional[float] = None,
-        aerosol_phase: Optional[Phase] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the WetDeposition object with the given parameters.
-
-        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.
-            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.other_properties = other_properties if other_properties is not None else self.other_properties
-
-
-class HenrysLaw(_HenrysLaw):
-    """
-    A class representing a Henry's law reaction rate constant.
-
-    Attributes:
-        name (str): The name of the Henry's law reaction rate constant.
-        gas_phase (Phase): The gas phase in which the reaction occurs.
-        gas_phase_species (Union[Species, Tuple[float, Species]]): The gas phase species involved in the reaction.
-        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-        aerosol_phase_water (Species): The water species in the aerosol phase.
-        aerosol_phase_species (Union[Species, Tuple[float, Species]]): The aerosol phase species involved in the reaction.
-        other_properties (Dict[str, Any]): A dictionary of other properties of the Henry's law reaction rate constant.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        gas_phase: Optional[Phase] = None,
-        gas_phase_species: Optional[Union[Species, Tuple[float, Species]]] = None,
-        aerosol_phase: Optional[Phase] = None,
-        aerosol_phase_water: Optional[Species] = None,
-        aerosol_phase_species: Optional[Union[Species, Tuple[float, Species]]] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the HenrysLaw object with the given parameters.
-
-        Args:
-            name (str): The name of the Henry's law reaction rate constant.
-            gas_phase (Phase): The gas phase in which the reaction occurs.
-            gas_phase_species (Union[Species, Tuple[float, Species]]): The gas phase species involved in the reaction.
-            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-            aerosol_phase_water (Species): The water species in the aerosol phase.
-            aerosol_phase_species (Union[Species, Tuple[float, Species]]): The aerosol phase species involved in the reaction.
-            other_properties (Dict[str, Any]): A dictionary of other properties of the Henry's law reaction rate constant.
-        """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
-        self.gas_phase_species = (
-            (
-                _ReactionComponent(gas_phase_species.name)
-                if isinstance(gas_phase_species, Species)
-                else _ReactionComponent(gas_phase_species[1].name, gas_phase_species[0])
-            )
-            if gas_phase_species is not None
-            else self.gas_phase_species
-        )
-        self.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
-        self.aerosol_phase_water = (
-            aerosol_phase_water.name if aerosol_phase_water is not None else self.aerosol_phase_water
-        )
-        self.aerosol_phase_species = (
-            (
-                _ReactionComponent(aerosol_phase_species.name)
-                if isinstance(aerosol_phase_species, Species)
-                else _ReactionComponent(
-                    aerosol_phase_species[1].name, aerosol_phase_species[0]
-                )
-            )
-            if aerosol_phase_species is not None
-            else self.aerosol_phase_species
-        )
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
-
-
-class SimpolPhaseTransfer(_SimpolPhaseTransfer):
-    """
-    A class representing a simplified phase transfer reaction rate constant.
-
-    Attributes:
-        name (str): The name of the simplified phase transfer reaction rate constant.
-        gas_phase (Phase): The gas phase in which the reaction occurs.
-        gas_phase_species (Union[Species, Tuple[float, Species]]): The gas phase species involved in the reaction.
-        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-        aerosol_phase_species (Union[Species, Tuple[float, Species]]): The aerosol phase species involved in the reaction.
-        B (List[float]): The B parameters [unitless].
-        unknown_properties (Dict[str, Any]): A dictionary of other properties of the simplified phase transfer reaction rate constant.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        gas_phase: Optional[Phase] = None,
-        gas_phase_species: Optional[Union[Species, Tuple[float, Species]]] = None,
-        aerosol_phase: Optional[Phase] = None,
-        aerosol_phase_species: Optional[Union[Species, Tuple[float, Species]]] = None,
-        B: Optional[List[float]] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the SimpolPhaseTransfer object with the given parameters.
-
-        Args:
-            name (str): The name of the simplified phase transfer reaction rate constant.
-            gas_phase (Phase): The gas phase in which the reaction occurs.
-            gas_phase_species (Union[Species, Tuple[float, Species]]): The gas phase species involved in the reaction.
-            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-            aerosol_phase_species (Union[Species, Tuple[float, Species]]): The aerosol phase species involved in the reaction.
-            B (List[float]): The B parameters [unitless].
-            other_properties (Dict[str, Any]): A dictionary of other properties of the simplified phase transfer reaction rate constant.
-        """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
-        self.gas_phase_species = (
-            (
-                _ReactionComponent(gas_phase_species.name)
-                if isinstance(gas_phase_species, Species)
-                else _ReactionComponent(gas_phase_species[1].name, gas_phase_species[0])
-            )
-            if gas_phase_species is not None
-            else self.gas_phase_species
-        )
-        self.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
-        self.aerosol_phase_species = (
-            (
-                _ReactionComponent(aerosol_phase_species.name)
-                if isinstance(aerosol_phase_species, Species)
-                else _ReactionComponent(
-                    aerosol_phase_species[1].name, aerosol_phase_species[0]
-                )
-            )
-            if aerosol_phase_species is not None
-            else self.aerosol_phase_species
-        )
-        if B is not None:
-            if len(B) != 4:
-                raise ValueError("B must be a list of 4 elements.")
-            self.B = B
-        else:
-            self.B = [0, 0, 0, 0]
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
-
-
-class UserDefined(_UserDefined):
-    """
-    A class representing a user-defined reaction rate constant.
-
-    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.
-    """
-
-    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.
-
-        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
-
-
-class Reactions(_Reactions):
-    """
-    A class representing a collection of reactions in a chemical mechanism.
-
-    Attributes:
-        reactions (List[Any]): A list of reactions in the mechanism.
-    """
-
-    def __init__(
-        self,
-        reactions: Optional[List[Any]] = None,
-    ):
-        """
-        Initializes the Reactions object with the given parameters.
-
-        Args:
-            reactions (List[]): A list of reactions in the mechanism.
-        """
-        super().__init__(reactions)
-
-
-class ReactionsIterator(_ReactionsIterator):
-    """
-    An iterator for the Reactions class.
-    """
-
-
-class Version(_Version):
-    """
-    A class representing the version of the mechanism.
-    """
-
-
-class Mechanism(_Mechanism):
-    """
-    A class representing a chemical mechanism.
-
-    Attributes:
-        name (str): The name of the mechanism.
-        reactions (List[Reaction]): A list of reactions in the mechanism.
-        species (List[Species]): A list of species in the mechanism.
-        phases (List[Phase]): A list of phases in the mechanism.
-        version (Version): The version of the mechanism.
-    """
-
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        reactions: Optional[List[Any]] = None,
-        species: Optional[List[Species]] = None,
-        phases: Optional[List[Phase]] = None,
-        version: Optional[Version] = None,
-    ):
-        """
-        Initializes the Mechanism object with the given parameters.
-
-        Args:
-            name (str): The name of the mechanism.
-            reactions (List[]): A list of reactions in the mechanism.
-            species (List[Species]): A list of species in the mechanism.
-            phases (List[Phase]): A list of phases in the mechanism.
-            version (Version): The version of the mechanism.
-        """
-        super().__init__()
-        self.name = name
-        self.species = species if species is not None else []
-        self.phases = phases if phases is not None else []
-        self.reactions = Reactions(reactions=reactions)
-        self.version = version if version is not None else Version()
-
-
-class Parser(_Parser):
-    """
-    A class for parsing a chemical mechanism.
-    """