from typing import Any, Optional
import numpy as np
from CADETProcess import CADETProcessError
from CADETProcess.dataStructure import (
Bool,
DependentlyModulatedUnsignedList,
RangedInteger,
SizedFloatList,
SizedRangedIntegerList,
SizedUnsignedIntegerList,
SizedUnsignedList,
String,
Structure,
UnsignedFloat,
UnsignedInteger,
frozen_attributes,
)
from .componentSystem import ComponentSystem
__all__ = [
"BindingBaseClass",
"NoBinding",
"Linear",
"Langmuir",
"LangmuirLDF",
"LangmuirLDFLiquidPhase",
"BiLangmuir",
"BiLangmuirLDF",
"FreundlichLDF",
"StericMassAction",
"AntiLangmuir",
"Spreading",
"MobilePhaseModulator",
"ExtendedMobilePhaseModulator",
"SelfAssociation",
"BiStericMassAction",
"MultistateStericMassAction",
"SimplifiedMultistateStericMassAction",
"Saska",
"GeneralizedIonExchange",
"HICUnified",
"HICConstantWaterActivity",
"HICWaterOnHydrophobicSurfaces",
"MultiComponentColloidal",
"AffinityComplexTitration",
]
[docs]
@frozen_attributes
class BindingBaseClass(Structure):
"""
Abstract base class for parameters of binding models.
Attributes
----------
name : str
name of the binding model.
component_system : ComponentSystem
system of components.
n_comp : int
number of components.
n_binding_sites : int
Number of binding sites.
Relevant for Multi-Site isotherms such as Bi-Langmuir.
The default is 1.
bound_states : list of unsigned integers.
Number of binding sites per component.
non_binding_component_indices : list
(Hardcoded) list of non binding modifier components (e.g. pH).
is_kinetic : bool
If False, adsorption is assumed to be in rapid equilibriu.
The default is True.
parameters : dict
dict with parameter values.
"""
name = String()
is_kinetic = Bool(default=True)
n_binding_sites = RangedInteger(lb=1, ub=1, default=1)
_bound_states = SizedRangedIntegerList(
size=("n_binding_sites", "n_comp"), lb=0, ub=1, default=1
)
non_binding_component_indices = []
_parameters = ["is_kinetic"]
def __init__(
self,
component_system: ComponentSystem,
name: Optional[str] = None,
*args: Any,
**kwargs: Any,
) -> None:
"""
Initialize binding model.
Parameters
----------
component_system: ComponentSystem
Component system of the binding model.
name: str
Name of the binding model.
"""
self.component_system = component_system
self.name = name
super().__init__(*args, **kwargs)
@property
def model(self) -> str:
"""str: Name of the binding model."""
return self.__class__.__name__
@property
def component_system(self) -> ComponentSystem:
"""ComponentSystem: Component system of the binding model."""
return self._component_system
@component_system.setter
def component_system(self, component_system: ComponentSystem) -> None:
if not isinstance(component_system, ComponentSystem):
raise TypeError("Expected ComponentSystem")
self._component_system = component_system
@property
def n_comp(self) -> int:
"""int: Number of components."""
return self.component_system.n_comp
@property
def bound_states(self) -> list[int]:
"""list[int]: Number of bound states per component."""
bound_states = self._bound_states
for i in self.non_binding_component_indices:
bound_states[i] = 0
return bound_states
@bound_states.setter
def bound_states(self, bound_states: np.ndarray) -> None:
indices = self.non_binding_component_indices
if any(bound_states[i] > 0 for i in indices):
raise CADETProcessError("Cannot set bound state for non-binding component.")
self._bound_states = bound_states
@property
def n_bound_states(self) -> int:
"""int: Number of bound states."""
return sum(self.bound_states)
def __repr__(self) -> str:
"""str: String representation of the binding model."""
return f"{self.__class__.__name__}(\
component_system={self.component_system}, name={self.name})')"
def __str__(self) -> str:
"""str: String representation of the binding model."""
if self.name is None:
return self.__class__.__name__
return self.name
[docs]
class NoBinding(BindingBaseClass):
"""
Dummy class for units that do not experience binging behavior.
The number of components is set to zero for this class.
"""
def __init__(self, *args: Any, **kwargs: Any) -> None:
"""Initialize NoBinding."""
super().__init__(ComponentSystem(), name="NoBinding")
[docs]
class Linear(BindingBaseClass):
"""
Linear binding model.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants. Length depends on `n_comp`.
desorption_rate : list of unsigned floats.
Desorption rate constants. Length depends on `n_comp`.
"""
adsorption_rate = SizedUnsignedList(size="n_comp")
desorption_rate = SizedUnsignedList(size="n_comp")
_parameters = [
"adsorption_rate",
"desorption_rate",
]
@property
def k_eq(self) -> list[float]:
"""list[float]: Equilibrium constant."""
return np.divide(self.adsorption_rate, self.desorption_rate).tolist()
@property
def henry_coefficient(self) -> list[float]:
"""list[float]: Henry coefficient."""
return self.k_eq
[docs]
class Langmuir(BindingBaseClass):
"""
Multi Component Langmuir binding model.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants. Length depends on `n_comp`.
desorption_rate : list of unsigned floats.
Desorption rate constants. Length depends on `n_comp`.
capacity : list of unsigned floats.
Maximum adsorption capacities. Length depends on `n_comp`.
"""
adsorption_rate = SizedUnsignedList(size="n_comp")
desorption_rate = SizedUnsignedList(size="n_comp")
capacity = SizedUnsignedList(size="n_comp")
_parameters = [
"adsorption_rate",
"desorption_rate",
"capacity",
]
@property
def k_eq(self) -> list[float]:
"""list[float]: Equilibrium constant."""
return np.divide(self.adsorption_rate, self.desorption_rate).tolist()
@property
def henry_coefficient(self) -> list[float]:
"""list[float]: Henry coefficient."""
return np.multiply(self.k_eq, self.capacity).tolist()
[docs]
class LangmuirLDF(BindingBaseClass):
"""
Multi Component Langmuir binding model with linear driving force approximation.
Note, this variant is based on the equilibrium concentration q* for given c.
Attributes
----------
equilibrium_constant : list of unsigned floats.
Adsorption rate constants. Length depends on `n_comp`.
driving_force_coefficient : list of unsigned floats.
Desorption rate constants. Length depends on `n_comp`.
capacity : list of unsigned floats.
Maximum adsorption capacities. Length depends on `n_comp`.
"""
equilibrium_constant = SizedUnsignedList(size="n_comp")
driving_force_coefficient = SizedUnsignedList(size="n_comp")
capacity = SizedUnsignedList(size="n_comp")
_parameters = [
"equilibrium_constant",
"driving_force_coefficient",
"capacity",
]
[docs]
class LangmuirLDFLiquidPhase(BindingBaseClass):
"""
Multi Component Langmuir binding model with linear driving force approximation.
Note, this variant is based on the equilibrium concentration c* for given q.
Attributes
----------
equilibrium_constant : list of unsigned floats.
Adsorption rate constants. Length depends on `n_comp`.
driving_force_coefficient : list of unsigned floats.
Desorption rate constants. Length depends on `n_comp`.
capacity : list of unsigned floats.
Maximum adsorption capacities. Length depends on `n_comp`.
"""
equilibrium_constant = SizedUnsignedList(size="n_comp")
driving_force_coefficient = SizedUnsignedList(size="n_comp")
capacity = SizedUnsignedList(size="n_comp")
_parameters = [
"equilibrium_constant",
"driving_force_coefficient",
"capacity",
]
[docs]
class BiLangmuir(BindingBaseClass):
"""
Multi Component Bi-Langmuir binding model.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants in state-major ordering.
Length depends on `n_bound_states`.
desorption_rate : list of unsigned floats.
Desorption rate constants in state-major ordering.
Length depends on `n_bound_states`.
capacity : list of unsigned floats.
Maximum adsorption capacities in state-major ordering.
Length depends on `n_bound_states`.
"""
n_binding_sites = UnsignedInteger(default=2)
adsorption_rate = SizedUnsignedList(size="n_bound_states")
desorption_rate = SizedUnsignedList(size="n_bound_states")
capacity = SizedUnsignedList(size="n_bound_states")
_parameters = [
"adsorption_rate",
"desorption_rate",
"capacity",
]
def __init__(self, *args: Any, n_binding_sites: int = 2, **kwargs: Any) -> None:
"""Initialize BiLangmuir."""
self.n_binding_sites = n_binding_sites
super().__init__(*args, **kwargs)
[docs]
class BiLangmuirLDF(BindingBaseClass):
"""
Multi Component Bi-Langmuir binding model.
Attributes
----------
equilibrium_constant : list of unsigned floats.
Adsorption rate constants in state-major ordering.
Length depends on `n_bound_states`.
driving_force_coefficient : list of unsigned floats.
Desorption rate constants in state-major ordering.
Length depends on `n_bound_states`.
capacity : list of unsigned floats.
Maximum adsorption capacities in state-major ordering.
Length depends on `n_bound_states`.
"""
n_binding_sites = UnsignedInteger(default=2)
equilibrium_constant = SizedUnsignedList(size="n_bound_states")
driving_force_coefficient = SizedUnsignedList(size="n_bound_states")
capacity = SizedUnsignedList(size="n_bound_states")
_parameters = [
"equilibrium_constant",
"driving_force_coefficient",
"capacity",
]
def __init__(self, *args: Any, n_binding_sites: int = 2, **kwargs: Any) -> None:
"""Initialize BiLangmuirLDF."""
self.n_binding_sites = n_binding_sites
super().__init__(*args, **kwargs)
[docs]
class FreundlichLDF(BindingBaseClass):
"""
Freundlich isotherm model.
Attributes
----------
driving_force_coefficient : list of unsigned floats.
Driving force coefficient for each component. Length depends on `n_comp`.
freundlich_coefficient : list of unsigned floats.
Freundlich coefficient for each component. Length depends on `n_comp`.
exponent : list of unsigned floats.
Freundlich exponent for each component. Length depends on `n_comp`.
"""
driving_force_coefficient = SizedUnsignedList(size="n_comp")
freundlich_coefficient = SizedUnsignedList(size="n_comp")
exponent = SizedUnsignedList(size="n_comp")
_parameters = [
"driving_force_coefficient",
"freundlich_coefficient",
"exponent",
]
[docs]
class StericMassAction(BindingBaseClass):
r"""
Steric Mass Action Law binding model.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants. Length depends on `n_comp`.
desorption_rate : list of unsigned floats.
Desorption rate constants. Length depends on `n_comp`.
characteristic_charge : list of unsigned floats.
Characteristic charges of the protein; The number of sites $\nu$ that the
protein interacts with on the resin surface.
Length depends on `n_comp`.
steric_factor : list of unsigned floats.
Steric factors of the protein: The number of sites $\sigma$ on the surface
that are shielded by the protein and prevented from exchange with salt
counterions in solution.
Length depends on `n_comp`.
capacity : unsigned float.
Stationary phase capacity (monovalent salt counterions); The total
number of binding sites available on the resin surface.
reference_liquid_phase_conc : unsigned float.
Reference liquid phase concentration.
The default is 1.0
reference_solid_phase_conc : unsigned float.
Reference liquid phase concentration.
The default is 1.0
"""
adsorption_rate = SizedUnsignedList(size="n_comp")
desorption_rate = SizedUnsignedList(size="n_comp")
characteristic_charge = SizedUnsignedList(size="n_comp")
steric_factor = SizedUnsignedList(size="n_comp")
capacity = UnsignedFloat()
reference_liquid_phase_conc = UnsignedFloat(default=1.0)
reference_solid_phase_conc = UnsignedFloat(default=1.0)
_parameters = [
"adsorption_rate",
"desorption_rate",
"characteristic_charge",
"steric_factor",
"capacity",
"reference_liquid_phase_conc",
"reference_solid_phase_conc",
]
@property
def adsorption_rate_untransformed(self) -> list[UnsignedFloat]:
"""list[float]: Untransformed adsorption rate."""
if self.adsorption_rate is None:
return None
nu = np.array(self.characteristic_charge)
return self.adsorption_rate * self.reference_solid_phase_conc ** (-nu)
@adsorption_rate_untransformed.setter
def adsorption_rate_untransformed(
self,
adsorption_rate_untransformed: list[float],
) -> None:
if self.characteristic_charge is None:
raise ValueError(
"Please set nu before setting an untransformed rate constant."
)
nu = np.array(self.characteristic_charge)
self.adsorption_rate = (
adsorption_rate_untransformed / self.reference_solid_phase_conc ** (-nu)
).tolist()
@property
def desorption_rate_untransformed(self) -> list[UnsignedFloat]:
"""list[float]: Untransformed desorption rate."""
if self.desorption_rate is None:
return None
nu = np.array(self.characteristic_charge)
return self.desorption_rate * self.reference_liquid_phase_conc ** (-nu)
@desorption_rate_untransformed.setter
def desorption_rate_untransformed(
self,
desorption_rate_untransformed: list[float],
) -> None:
if self.characteristic_charge is None:
raise ValueError(
"Please set nu before setting a transformed rate constant."
)
nu = np.array(self.characteristic_charge)
self.desorption_rate = (
desorption_rate_untransformed / self.reference_liquid_phase_conc ** (-nu)
).tolist()
[docs]
class AntiLangmuir(BindingBaseClass):
"""
Multi Component Anti-Langmuir adsorption isotherm.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants. Length depends on `n_comp`.
desorption_rate : list of unsigned floats
Desorption rate constants. Length depends on `n_comp`.
capacity : list of unsigned floats.
Maximum adsorption capacities. Length depends on `n_comp`.
antilangmuir : list of {-1, 1}.
Anti-Langmuir coefficients. Length depends on `n_comp`.
"""
adsorption_rate = SizedUnsignedList(size="n_comp")
desorption_rate = SizedUnsignedList(size="n_comp")
capacity = SizedUnsignedList(size="n_comp")
antilangmuir = SizedFloatList(size="n_comp")
_parameters = ["adsorption_rate", "desorption_rate", "capacity", "antilangmuir"]
[docs]
class Spreading(BindingBaseClass):
"""
Multi Component Spreading adsorption isotherm.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants in state-major ordering.
Length depends on `n_bound_states`.
desorption_rate : list of unsigned floats.
Desorption rate constants in state-major ordering.
Length depends on `n_bound_states`.
capacity : list of unsigned floats.
Maximum adsorption capacities in state-major ordering.
Length depends on `n_bound_states`.
exchange_from_1_2 : list of unsigned floats.
Exchange rates from the first to the second bound state.
Length depends on `n_comp`.
exchange_from_2_1 : list of unsigned floats.
Exchange rates from the second to the first bound state.
Length depends on `n_comp`.
"""
n_binding_sites = RangedInteger(lb=2, ub=2, default=2)
adsorption_rate = SizedUnsignedList(size="n_bound_states")
desorption_rate = SizedUnsignedList(size="n_bound_states")
capacity = SizedUnsignedList(size="n_bound_states")
exchange_from_1_2 = SizedUnsignedList(size="n_comp")
exchange_from_2_1 = SizedUnsignedList(size="n_comp")
_parameters = [
"adsorption_rate",
"desorption_rate",
"capacity",
"exchange_from_1_2",
"exchange_from_2_1",
]
[docs]
class MobilePhaseModulator(BindingBaseClass):
"""
Mobile Phase Modulator adsorption isotherm.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants. Length depends on `n_comp`.
desorption_rate : list of unsigned floats.
Desorption rate constants. Length depends on `n_comp`.
capacity : list of unsigned floats.
Maximum adsorption capacities. Length depends on `n_comp`.
ion_exchange_characteristic : list of unsigned floats.
Parameters describing the ion-exchange characteristics (IEX).
Length depends on `n_comp`.
hydrophobicity : list of floats.
Parameters describing the hydrophobicity (HIC).
Length depends on `n_comp`.
linear_threshold : UnsignedFloat
Concentration of c0 at which to switch to linear model approximation.
"""
adsorption_rate = SizedUnsignedList(size="n_comp")
desorption_rate = SizedUnsignedList(size="n_comp")
capacity = SizedUnsignedList(size="n_comp")
ion_exchange_characteristic = SizedUnsignedList(size="n_comp")
beta = ion_exchange_characteristic
hydrophobicity = SizedFloatList(size="n_comp")
gamma = hydrophobicity
linear_threshold = UnsignedFloat(default=1e-8)
_parameters = [
"adsorption_rate",
"desorption_rate",
"capacity",
"ion_exchange_characteristic",
"hydrophobicity",
"linear_threshold",
]
[docs]
class ExtendedMobilePhaseModulator(BindingBaseClass):
"""
Mobile Phase Modulator adsorption isotherm.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants. Length depends on `n_comp`.
desorption_rate : list of unsigned floats.
Desorption rate constants. Length depends on `n_comp`.
capacity : list of unsigned floats.
Maximum adsorption capacities. Length depends on `n_comp`.
ion_exchange_characteristic : list of unsigned floats.
Parameters describing the ion-exchange characteristics (IEX).
Length depends on `n_comp`.
hydrophobicity : list of floats.
Parameters describing the hydrophobicity (HIC).
Length depends on `n_comp`.
component_mode : list of unsigned integers.
Mode of each component;
0 denotes the modifier component,
1 is linear binding,
2 is modified Langmuir binding.
Length depends on `n_comp`.
"""
adsorption_rate = SizedUnsignedList(size="n_comp")
desorption_rate = SizedUnsignedList(size="n_comp")
capacity = SizedUnsignedList(size="n_comp")
ion_exchange_characteristic = SizedUnsignedList(size="n_comp")
beta = ion_exchange_characteristic
hydrophobicity = SizedFloatList(size="n_comp")
gamma = hydrophobicity
component_mode = SizedUnsignedIntegerList(size="n_comp", ub=2)
_parameters = [
"adsorption_rate",
"desorption_rate",
"capacity",
"ion_exchange_characteristic",
"hydrophobicity",
"component_mode",
]
[docs]
class SelfAssociation(BindingBaseClass):
r"""
Self Association adsorption isotherm.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants. Length depends on `n_comp`.
adsorption_rate_dimerization : list of unsigned floats.
Adsorption rate constants of dimerization. Length depends on `n_comp`.
desorption_rate : list of unsigned floats.
Desorption rate constants. Length depends on `n_comp`.
characteristic_charge : list of unsigned floats.
The characteristic charge $\nu$ of the protein. Length depends on `n_comp`.
steric_factor : list of unsigned floats.
Steric factor of of the protein. Length depends on `n_comp`.
capacity : unsigned float.
Stationary phase capacity (monovalent salt counterions); The total number of
binding sites available on the resin surface.
reference_liquid_phase_conc : unsigned float.
Reference liquid phase concentration (optional, default value = 1.0).
The default = 1.0
reference_solid_phase_conc : unsigned float.
Reference liquid phase concentration (optional)
The default = 1.0
"""
adsorption_rate = SizedUnsignedList(size="n_comp")
adsorption_rate_dimerization = SizedUnsignedList(size="n_comp")
desorption_rate = SizedUnsignedList(size="n_comp")
characteristic_charge = SizedUnsignedList(size="n_comp")
steric_factor = SizedUnsignedList(size="n_comp")
capacity = UnsignedFloat()
reference_liquid_phase_conc = UnsignedFloat(default=1.0)
reference_solid_phase_conc = UnsignedFloat(default=1.0)
_parameters = [
"adsorption_rate",
"adsorption_rate_dimerization",
"desorption_rate",
"characteristic_charge",
"steric_factor",
"capacity",
"reference_liquid_phase_conc",
"reference_solid_phase_conc",
]
[docs]
class BiStericMassAction(BindingBaseClass):
"""
Bi Steric Mass Action adsorption isotherm.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants in state-major ordering.
Length depends on `n_bound_states`.
desorption_rate : list of unsigned floats.
Desorption rate constants in state-major ordering.
Length depends on `n_bound_states`.
characteristic_charge : list of unsigned floats.
Characteristic charges v(i,j) of the it-h protein with respect to the
j-th binding site type in state-major ordering.
Length depends on `n_bound_states`.
steric_factor : list of unsigned floats.
Steric factor o (i,j) of the it-h protein with respect to the j-th
binding site type in state-major ordering.
Length depends on `n_bound_states`.
capacity : unsigned float.
Stationary phase capacity (monovalent salt counterions); The total
number of binding sites available on the resin surface.
Length depends on `n_binding_sites`.
reference_liquid_phase_conc : list of unsigned floats.
Reference liquid phase concentration for each binding site type or one
value for all types.
The default is 1.0
reference_solid_phase_conc : list of unsigned floats.
Reference solid phase concentration for each binding site type or one
value for all types.
The default is 1.0
"""
n_binding_sites = UnsignedInteger(default=2)
adsorption_rate = SizedUnsignedList(size="n_bound_states")
adsorption_rate_dimerization = SizedUnsignedList(size="n_bound_states")
desorption_rate = SizedUnsignedList(size="n_bound_states")
characteristic_charge = SizedUnsignedList(size="n_bound_states")
steric_factor = SizedUnsignedList(size="n_bound_states")
capacity = SizedUnsignedList(size="n_binding_sites")
reference_liquid_phase_conc = SizedUnsignedList(size="n_binding_sites", default=1)
reference_solid_phase_conc = SizedUnsignedList(size="n_binding_sites", default=1)
_parameters = [
"adsorption_rate",
"desorption_rate",
"characteristic_charge",
"steric_factor",
"capacity",
"reference_liquid_phase_conc",
"reference_solid_phase_conc",
]
def __init__(self, *args: Any, n_states: int = 2, **kwargs: Any) -> None:
"""Initialize BiStericMassAction class."""
self.n_states = n_states
super().__init__(*args, **kwargs)
[docs]
class MultistateStericMassAction(BindingBaseClass):
r"""
Multistate Steric Mass Action adsorption isotherm.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants of the components to different bound states in
component-major ordering.
Length depends on `n_bound_states`.
desorption_rate : list of unsigned floats.
Desorption rate constants of the components to different bound states in
component-major ordering.
Length depends on `n_bound_states`.
characteristic_charge : list of unsigned floats.
Characteristic charges of the components to different bound states in
component-major ordering.
Length depends on `n_bound_states`.
steric_factor : list of unsigned floats.
Steric factor of the components to different bound states in component-major
ordering.
Length depends on `n_bound_states`.
conversion_rate : list of unsigned floats.
Conversion rates between different bound states in
component-major ordering.
Length: $sum_{i=1}^{n_{comp}} n_{bound, i}$
capacity : unsigned float.
Stationary phase capacity (monovalent salt counterions); The total number of
binding sites available on the resin surface.
reference_liquid_phase_conc : unsigned float.
Reference liquid phase concentration.
The default = 1.0
reference_solid_phase_conc : unsigned float, optional
Reference solid phase concentration.
The default = 1.0
"""
bound_states = SizedUnsignedIntegerList(
size=("n_binding_sites", "n_comp"), default=1
)
adsorption_rate = SizedUnsignedList(size="n_bound_states")
desorption_rate = SizedUnsignedList(size="n_bound_states")
characteristic_charge = SizedUnsignedList(size="n_bound_states")
steric_factor = SizedUnsignedList(size="n_bound_states")
conversion_rate = SizedUnsignedList(size="_conversion_entries")
capacity = UnsignedFloat()
reference_liquid_phase_conc = UnsignedFloat(default=1)
reference_solid_phase_conc = UnsignedFloat(default=1)
_parameters = [
"adsorption_rate",
"desorption_rate",
"characteristic_charge",
"steric_factor",
"conversion_rate",
"capacity",
"reference_liquid_phase_conc",
"reference_solid_phase_conc",
]
@property
def _conversion_entries(self) -> int:
n = 0
for state in self.bound_states:
n += state ** 2
return n
[docs]
class SimplifiedMultistateStericMassAction(BindingBaseClass):
"""
Simplified multistate Steric Mass Action adsorption isotherm.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants of the components to different bound states
in component-major ordering.
Length depends on `n_bound_states`.
desorption_rate : list of unsigned floats.
Desorption rate constants of the components to different bound states
in component-major ordering.
Length depends on `n_bound_states`.
characteristic_charge_first : list of unsigned floats.
Characteristic charges of the components in the first (weakest) bound state.
Length depends on `n_comp`.
characteristic_charge_last : list of unsigned floats.
Characteristic charges of the components in the last (strongest) bound state.
Length depends on `n_comp`.
quadratic_modifiers_charge : list of unsigned floats.
Quadratic modifiers of the characteristic charges of the different components
depending on the index of the bound state.
Length depends on `n_comp`.
steric_factor_first : list of unsigned floats.
Steric factor of the components in the first (weakest) bound state.
Length depends on `n_comp`.
steric_factor_last : list of unsigned floats.
Steric factor of the components in the last (strongest) bound state.
Length depends on `n_comp`.
quadratic_modifiers_steric : list of unsigned floats.
Quadratic modifiers of the sterif factors of the different components depending
on the index of the bound state.
Length depends on `n_comp`.
capacity : unsigned float.
Stationary phase capacity (monovalent salt counterions): The total number of
binding sites available on the resin surface.
exchange_from_weak_stronger : list of unsigned floats.
Exchangde rated from a weakly bound state to the next stronger bound state.
linear_exchange_ws : list of unsigned floats.
Linear exchange rate coefficients from a weakly bound state to the next stronger
bound state.
Length depends on `n_comp`.
quadratic_exchange_ws : list of unsigned floats.
Quadratic exchange rate coefficients from a weakly bound state to the next
stronger bound state.
Length depends on `n_comp`.
exchange_from_stronger_weak : list of unsigned floats.
Exchange rate coefficients from a strongly bound state to the next weaker bound
state.
Length depends on `n_comp`.
linear_exchange_sw : list of unsigned floats.
Linear exchange rate coefficients from a strongly bound state to the next weaker
bound state.
Length depends on `n_comp`.
quadratic_exchange_sw : list of unsigned floats.
Quadratic exchange rate coefficients from a strongly bound state to the next
weaker bound state.
Length depends on `n_comp`.
reference_liquid_phase_conc : list of unsigned floats.
Reference liquid phase concentration (optional, default value = 1.0).
reference_solid_phase_conc : list of unsigned floats.
Reference solid phase concentration (optional, default value = 1.0).
"""
bound_states = SizedUnsignedIntegerList(
size=("n_binding_sites", "n_comp"), default=1
)
adsorption_rate = SizedUnsignedList(size="n_bound_states")
desorption_rate = SizedUnsignedList(size="n_bound_states")
characteristic_charge_first = SizedUnsignedList(size="n_comp")
characteristic_charge_last = SizedUnsignedList(size="n_comp")
quadratic_modifiers_charge = SizedUnsignedList(size="n_comp")
steric_factor_first = SizedUnsignedList(size="n_comp")
steric_factor_last = SizedUnsignedList(size="n_comp")
quadratic_modifiers_steric = SizedUnsignedList(size="n_comp")
capacity = UnsignedFloat()
exchange_from_weak_stronger = SizedUnsignedList(size="n_comp")
linear_exchange_ws = SizedUnsignedList(size="n_comp")
quadratic_exchange_ws = SizedUnsignedList(size="n_comp")
exchange_from_stronger_weak = SizedUnsignedList(size="n_comp")
linear_exchange_sw = SizedUnsignedList(size="n_comp")
quadratic_exchange_sw = SizedUnsignedList(size="n_comp")
reference_liquid_phase_conc = UnsignedFloat(default=1)
reference_solid_phase_conc = UnsignedFloat(default=1)
_parameters = [
"adsorption_rate",
"desorption_rate",
"characteristic_charge_first",
"characteristic_charge_last",
"quadratic_modifiers_charge",
"steric_factor_first",
"steric_factor_last",
"quadratic_modifiers_steric",
"capacity",
"exchange_from_weak_stronger",
"linear_exchange_ws",
"quadratic_exchange_ws",
"exchange_from_stronger_weak",
"linear_exchange_sw",
"quadratic_exchange_sw",
"reference_liquid_phase_conc",
"reference_solid_phase_conc",
]
[docs]
class Saska(BindingBaseClass):
"""
Quadratic Isotherm.
Attributes
----------
henry_const : list of unsigned floats.
The Henry coefficient. Length depends on `n_comp`.
quadratic_factor : list of unsigned floats.
Quadratic factors. Length depends on `n_comp`.
"""
henry_const = SizedUnsignedList(size="n_comp")
quadratic_factor = SizedUnsignedList(size=("n_comp", "n_comp"))
_parameters = [
"henry_const",
"quadratic_factor",
]
[docs]
class GeneralizedIonExchange(BindingBaseClass):
r"""
Generalized Ion Exchange isotherm model.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants. Length depends on `n_comp`.
adsorption_rate_linear : list of unsigned floats.
Linear dependence coefficient of adsorption rate on modifier component
Length depends on `n_comp`.
adsorption_rate_quadratic : list of unsigned floats.
Quadratic dependence coefficient of adsorption rate on modifier component.
Length depends on `n_comp`.
adsorption_rate_cubic : list of unsigned floats.
Cubic dependence coefficient of adsorption rate on modifier component.
Length depends on `n_comp`.
adsorption_rate_salt : list of unsigned floats.
Salt coefficient of adsorption rate;
difference of water-protein and salt-protein interactions.
Length depends on `n_comp`.
adsorption_rate_protein : list of unsigned floats.
Protein coefficient of adsorption rate;
difference of water-protein and protein-protein interactions.
Length depends on `n_comp`.
desorption_rate : list of unsigned floats.
Desorption rate constants. Length depends on `n_comp`.
desorption_rate_linear : list of unsigned floats.
Linear dependence coefficient of desorption rate on modifier component.
Length depends on `n_comp`.
desorption_rate_quadratic : list of unsigned floats.
Quadratic dependence coefficient of desorption rate on modifier component.
Length depends on `n_comp`.
desorption_rate_cubic : list of unsigned floats.
Cubic dependence coefficient of desorption rate on modifier component.
Length depends on `n_comp`.
desorption_rate_salt : list of unsigned floats.
Salt coefficient of desorption rate;
difference of water-protein and salt-protein interactions.
Length depends on `n_comp`.
desorption_rate_protein : list of unsigned floats.
Protein coefficient of desorption rate;
difference of water-protein and protein-protein interactions
Length depends on `n_comp`.
characteristic_charge_breaks : list of unsigned floats, optional
Breaks of the characteristic charge pieces in component-major ordering.
Optional, only required if a piecewise cubic polynomial is used for $\nu$.
Length must be a multiple of `n_comp`.
characteristic_charge : list of unsigned floats.
Base value for characteristic charges of the protein; The number of sites $\nu$
that the protein interacts with on the resin surface.
Length depends on `n_comp` * `n_pieces`.
characteristic_charge_linear : list of unsigned floats.
Linear dependence coefficient of characteristic charge on modifier component.
Length depends on `n_comp` * `n_pieces`.
characteristic_charge_quadratic : list of unsigned floats.
Quadratic dependence coefficient of characteristic charge on modifier component.
Length depends on `n_comp` * `n_pieces`.
characteristic_charge_cubic : list of unsigned floats.
Cubic dependence coefficient of characteristic charge on modifier component.
Length depends on `n_comp` * `n_pieces`.
steric_factor : list of unsigned floats.
Steric factors of the protein: The number of sites $\sigma$ on the surface that
are shielded by the protein and prevented from exchange with salt counterions in
solution.
Length depends on `n_comp`.
capacity : unsigned float.
Stationary phase capacity (monovalent salt counterions); The total number of
binding sites available on the resin surface.
reference_liquid_phase_conc : unsigned float.
Reference liquid phase concentration (optional, default value = 1.0).
reference_solid_phase_conc : unsigned float.
Reference liquid phase concentration (optional, default value = 1.0).
"""
non_binding_component_indices = [1]
adsorption_rate = SizedFloatList(size="n_comp")
adsorption_rate_linear = SizedFloatList(size="n_comp", default=0)
adsorption_rate_quadratic = SizedFloatList(size="n_comp", default=0)
adsorption_rate_cubic = SizedFloatList(size="n_comp", default=0)
adsorption_rate_salt = SizedFloatList(size="n_comp", default=0)
adsorption_rate_protein = SizedFloatList(size="n_comp", default=0)
desorption_rate = SizedFloatList(size="n_comp")
desorption_rate_linear = SizedFloatList(size="n_comp", default=0)
desorption_rate_quadratic = SizedFloatList(size="n_comp", default=0)
desorption_rate_cubic = SizedFloatList(size="n_comp", default=0)
desorption_rate_salt = SizedFloatList(size="n_comp", default=0)
desorption_rate_protein = SizedFloatList(size="n_comp", default=0)
characteristic_charge_breaks = DependentlyModulatedUnsignedList(
size="n_comp", is_optional=True
)
characteristic_charge = SizedFloatList(
size=("n_pieces", "n_comp"),
)
characteristic_charge_linear = SizedFloatList(
size=("n_pieces", "n_comp"), default=0
)
characteristic_charge_quadratic = SizedFloatList(
size=("n_pieces", "n_comp"), default=0
)
characteristic_charge_cubic = SizedFloatList(size=("n_pieces", "n_comp"), default=0)
steric_factor = SizedUnsignedList(size="n_comp")
capacity = UnsignedFloat()
reference_liquid_phase_conc = UnsignedFloat(default=1)
reference_solid_phase_conc = UnsignedFloat(default=1)
_parameters = [
"adsorption_rate",
"adsorption_rate_linear",
"adsorption_rate_quadratic",
"adsorption_rate_cubic",
"adsorption_rate_salt",
"adsorption_rate_protein",
"desorption_rate",
"desorption_rate_linear",
"desorption_rate_quadratic",
"desorption_rate_cubic",
"desorption_rate_salt",
"desorption_rate_protein",
"characteristic_charge_breaks",
"characteristic_charge",
"characteristic_charge_linear",
"characteristic_charge_quadratic",
"characteristic_charge_cubic",
"steric_factor",
"capacity",
"reference_liquid_phase_conc",
"reference_solid_phase_conc",
]
@property
def n_pieces(self) -> int:
"""int: Number of pieces for cubic polynomial description of nu."""
if self.characteristic_charge_breaks is None:
return 1
n_pieces_all = len(self.characteristic_charge_breaks) - self.n_comp
n_pieces_comp = int(n_pieces_all / self.n_comp)
return n_pieces_comp
[docs]
class HICConstantWaterActivity(BindingBaseClass):
"""
HIC based on Constant Water Activity adsorption isotherm.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants. Size depends on `n_comp`.
desorption_rate : list of unsigned floats.
Desorption rate constants. Size depends on `n_comp`.
capacity : list of unsigned floats.
Maximum adsorption capacities. Size depends on `n_comp`.
hic_characteristic : list of unsigned floats.
Parameters describing the number of ligands per ligand-protein interaction.
Size depends on `n_comp`.
beta_0 : unsigned float.
Parameter describing the number of highly ordered water molecules that stabilize
the hydrophobic surfaces at infinitely diluted salt concentration.
beta_1 : unsigned float.
Parameter describing the change in the number of highly ordered water molecules that
stabilize the hydrophobic surfaces with respect to changes in the salt concentration.
"""
adsorption_rate = SizedFloatList(size="n_comp")
desorption_rate = SizedFloatList(size="n_comp")
capacity = SizedFloatList(size="n_comp")
hic_characteristic = SizedFloatList(size="n_comp")
beta_0 = UnsignedFloat()
beta_1 = UnsignedFloat()
_parameters = [
"adsorption_rate",
"desorption_rate",
"hic_characteristic",
"capacity",
"beta_0",
"beta_1",
]
class HICUnified(BindingBaseClass):
"""HIC based on Constant Water Activity adsorption isotherm.
Attributes
----------
adsorption_rate : list of unsigned floats
Adsorption rate constants. Size depends on `n_comp`.
desorption_rate : list of unsigned floats.
Desorption rate constants. Size depends on `n_comp`.
capacity : list of unsigned floats
Maximum adsorption capacities. Size depends on `n_comp`.
hic_characteristic : list of unsigned floats.
Parameters describing the number of ligands per ligand-protein interaction.
Size depends on `n_comp`.
beta_0 : unsigned float
Parameter describing the number of highly ordered water molecules that stabilize
the hydrophobic surfaces at infinitely diluted salt concentration.
beta_1 : unsigned float
Parameter describing the change in the number of highly ordered water molecules
that stabilize the hydrophobic surfaces with respect to changes in the salt
concentration.
reference_liquid_phase_conc_c1 : unsigned float.
Reference for component 1 (optional, defaults to :math:`0.0`)
rho : unsigned float
Osmotic effect of :math:`c_0` on the water activity,
calculated as osmotic_coefficient * molar_weight_of_water * ion_number.
Optional, defaults to 3.35e-5 for NaCl
"""
adsorption_rate = SizedFloatList(size="n_comp")
adsorption_rate_linear = SizedFloatList(size="n_comp")
desorption_rate = SizedFloatList(size="n_comp")
protein_coefficient = SizedFloatList(size="n_comp")
salt_coefficient = SizedFloatList(size="n_comp")
bound_protein_coefficient = SizedFloatList(size="n_comp")
hic_characteristic = SizedFloatList(size="n_comp")
hic_characteristic_linear = SizedFloatList(size="n_comp")
capacity = SizedFloatList(size="n_comp")
beta_0 = UnsignedFloat()
beta_1 = UnsignedFloat()
reference_liquid_phase_conc_c1 = UnsignedFloat(default=0.0)
rho = UnsignedFloat(degault=3.35e-5)
_parameters = [
"adsorption_rate",
"adsorption_rate_linear",
"desorption_rate",
"protein_coefficient",
"salt_coefficient",
"bound_protein_coefficient",
"hic_characteristic",
"hic_characteristic_linear",
"capacity",
"beta_0",
"beta_1",
"reference_liquid_phase_conc_c1",
"rho",
]
[docs]
class HICWaterOnHydrophobicSurfaces(BindingBaseClass):
"""
HIC isotherm by Wang et al. based on their 2016 paper.
Attributes
----------
adsorption_rate : list of unsigned floats.
Adsorption rate constants. Size depends on `n_comp`.
desorption_rate : list of unsigned floats.
Desorption rate constants. Size depends on `n_comp`.
capacity : list of unsigned floats.
Maximum adsorption capacities. Size depends on `n_comp`.
hic_characteristic : list of unsigned floats.
Parameters describing the number of ligands per ligand-protein interaction.
Size depends on `n_comp`.
beta_0 : unsigned float.
Parameter describing the number of highly ordered water molecules that stabilize
the hydrophobic surfaces at infinitely diluted salt concentration.
beta_1 : unsigned float.
Parameter describing the change in the number of highly ordered water molecules that
stabilize the hydrophobic surfaces with respect to changes in the salt concentration.
"""
adsorption_rate = SizedFloatList(size="n_comp")
desorption_rate = SizedFloatList(size="n_comp")
capacity = SizedFloatList(size="n_comp")
hic_characteristic = SizedFloatList(size="n_comp")
beta_0 = UnsignedFloat()
beta_1 = UnsignedFloat()
_parameters = [
"adsorption_rate",
"desorption_rate",
"hic_characteristic",
"capacity",
"beta_0",
"beta_1",
]
[docs]
class MultiComponentColloidal(BindingBaseClass):
"""
Colloidal isotherm from Xu and Lenhoff 2009.
Attributes
----------
phase_ratio : unsigned float.
Phase ratio.
kappa_exponential : unsigned float.
Screening term exponential factor.
kappa_factor : unsigned float.
Screening term factor.
kappa_constant : unsigned float.
Screening term constant.
coordination_number : unsigned integer.
Coordination number.
logkeq_ph_exponent : list of unsigned floats.
Equilibrium constant factor exponent term for pH. Size depends on `n_comp`.
logkeq_power_exponent : list of unsigned floats.
Equilibrium constant power exponent term for salt. Size depends on `n_comp`.
logkeq_power_factor : list of unsigned floats.
Equilibrium constant power factor term for salt. Size depends on `n_comp`.
logkeq_exponent_factor : list of unsigned floats.
Equilibrium constant exponent factor term for salt. Size depends on `n_comp`.
logkeq_exponent_multiplier : list of unsigned floats.
Equilibrium constant exponent multiplier term for salt. Size depends on `n_comp`.
bpp_ph_exponent : list of unsigned floats..
BPP constant exponent factor term for pH. Size depends on `n_comp`.
bpp_power_exponent : list of unsigned floats.
Bpp constant power exponent term for salt. Size depends on `n_comp`.
bpp_power_factor : list of unsigned floats.
Bpp constant power factor term for salt. Size depends on `n_comp`.
bpp_exponent_factor : list of unsigned floats.
Bpp constant exponent factor term for salt. Size depends on `n_comp`.
bpp_exponent_multiplier : list of unsigned floats.
Bpp constant exponent multiplier term for salt. Size depends on `n_comp`.
protein_radius : list of unsigned floats.
Protein radius. Size depends on `n_comp`.
kinetic_rate_constant : list of unsigned floats.
Adsorption kinetics. Size depends on `n_comp`.
linear_threshold : unsigned float.
Linear threshold.
use_ph : Boolean.
Include pH or not.
"""
bound_states = SizedUnsignedIntegerList(
size=("n_binding_sites", "n_comp"), default=1
)
phase_ratio = UnsignedFloat()
kappa_exponential = UnsignedFloat()
kappa_factor = UnsignedFloat()
kappa_constant = UnsignedFloat()
coordination_number = UnsignedInteger()
logkeq_ph_exponent = SizedFloatList(size="n_comp")
logkeq_power_exponent = SizedFloatList(size="n_comp")
logkeq_power_factor = SizedFloatList(size="n_comp")
logkeq_exponent_factor = SizedFloatList(size="n_comp")
logkeq_exponent_multiplier = SizedFloatList(size="n_comp")
bpp_ph_exponent = SizedFloatList(size="n_comp")
bpp_power_exponent = SizedFloatList(size="n_comp")
bpp_power_factor = SizedFloatList(size="n_comp")
bpp_exponent_factor = SizedFloatList(size="n_comp")
bpp_exponent_multiplier = SizedFloatList(size="n_comp")
protein_radius = SizedFloatList(size="n_comp")
kinetic_rate_constant = SizedFloatList(size="n_comp")
linear_threshold = UnsignedFloat(default=1e-8)
use_ph = Bool(default=False)
_parameters = [
"phase_ratio",
"kappa_exponential",
"kappa_factor",
"kappa_constant",
"coordination_number",
"logkeq_ph_exponent",
"logkeq_power_exponent",
"logkeq_power_factor",
"logkeq_exponent_factor",
"logkeq_exponent_multiplier",
"bpp_ph_exponent",
"bpp_power_exponent",
"bpp_power_factor",
"bpp_exponent_factor",
"bpp_exponent_multiplier",
"protein_radius",
"kinetic_rate_constant",
"linear_threshold",
"use_ph",
]
class AffinityComplexTitration(BindingBaseClass):
"""
Colloidal isotherm from Xu and Lenhoff 2009.
Attributes
----------
adsorption_rate: list of unsigned floats.
Adsorption rate. Size depends on `n_comp`.
desorption_rate: list of unsigned floats.
Desorption rate. Size depends on `n_comp`.
capacity: list of unsigned floats.
Maximum adsorption capacities. Length depends on `n_comp`.
eta_a: list of unsigned floats.
Hill-type coefficients denoting the slope for the binding capacity changes as a
function of pH changes. Length depends on `n_comp`.
eta_g: list of unsigned floats.
Hill-type coefficients denoting the slope for the equilibrium constant changes
as a function of pH changes. Length depends on `n_comp`.
pka_a: list of unsigned floats.
Center point for the binding capacity changes as a function of pH changes.
Length depends on `n_comp`.
pka_g: list of unsigned floats.
Center point for the equilibrium constant changes as a function of pH changes.
Length depends on `n_comp`.
"""
adsorption_rate = SizedFloatList(size="n_comp")
desorption_rate = SizedFloatList(size="n_comp")
capacity = SizedUnsignedList(size="n_comp")
eta_a = SizedUnsignedList(size="n_comp")
eta_g = SizedUnsignedList(size="n_comp")
pka_a = SizedUnsignedList(size="n_comp")
pka_g = SizedUnsignedList(size="n_comp")
_parameters = [
"adsorption_rate",
"desorption_rate",
"capacity",
"eta_a",
"eta_g",
"pka_a",
"pka_g",
]
