from warnings import warn
import numpy as np
from CADETProcess import CADETProcessError
from CADETProcess.dataStructure import frozen_attributes
from CADETProcess.dataStructure import Structure
from CADETProcess.dataStructure import (
Bool, String,
RangedInteger, UnsignedInteger, UnsignedFloat, SizedList,
SizedRangedIntegerList, SizedUnsignedIntegerList,
SizedUnsignedList,
DependentlyModulatedUnsignedList
)
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',
'HICConstantWaterActivity',
'HICWaterOnHydrophobicSurfaces',
]
[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, name=None, *args, **kwargs):
self.component_system = component_system
self.name = name
super().__init__(*args, **kwargs)
@property
def model(self):
return self.__class__.__name__
@property
def component_system(self):
return self._component_system
@component_system.setter
def component_system(self, component_system):
if not isinstance(component_system, ComponentSystem):
raise TypeError('Expected ComponentSystem')
self._component_system = component_system
@property
def n_comp(self):
return self.component_system.n_comp
@property
def bound_states(self):
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):
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):
return sum(self.bound_states)
def __repr__(self):
return f"{self.__class__.__name__}(\
component_system={self.component_system}, name={self.name})')"
def __str__(self):
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, **kwargs):
super().__init__(ComponentSystem(), name='NoBinding')
[docs]
class Linear(BindingBaseClass):
"""Parameters for 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',
]
[docs]
class Langmuir(BindingBaseClass):
"""Parameters for 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',
]
[docs]
class LangmuirLDF(BindingBaseClass):
"""Parameters for Multi Component Langmuir binding model using a linear driving
force approximation 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',
]
class LangmuirLDFLiquidPhase(BindingBaseClass):
"""Parameters for Multi Component Langmuir binding model using a linear driving
force approximation 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):
"""Parameters for 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, n_binding_sites=2, **kwargs):
self.n_binding_sites = n_binding_sites
super().__init__(*args, **kwargs)
[docs]
class BiLangmuirLDF(BindingBaseClass):
"""Parameters for 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, n_binding_sites=2, **kwargs):
self.n_binding_sites = n_binding_sites
super().__init__(*args, **kwargs)
[docs]
class FreundlichLDF(BindingBaseClass):
"""Parameters for the 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):
"""Parameters for 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):
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):
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):
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):
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 unsigned floats, optional.
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 = SizedUnsignedList(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_total_bound`.
desorption_rate : list of unsigned floats.
Desorption rate constants in state-major ordering.
Length depends on `n_total_bound`.
capacity : list of unsigned floats.
Maximum adsorption capacities in state-major ordering.
Length depends on `n_total_bound`.
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_total_bound')
desorption_rate = SizedUnsignedList(size='n_total_bound')
capacity = SizedUnsignedList(size='n_total_bound')
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'
]
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 unsigned floats.
Parameters describing the hydrophobicity (HIC).
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 = SizedUnsignedList(size='n_comp')
gamma = hydrophobicity
_parameters = [
'adsorption_rate',
'desorption_rate',
'capacity',
'ion_exchange_characteristic',
'hydrophobicity',
]
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 unsigned 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 = SizedUnsignedList(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):
"""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, n_states=2, **kwargs):
self.n_states = n_states
super().__init__(*args, **kwargs)
[docs]
class MultistateStericMassAction(BindingBaseClass):
"""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):
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):
"""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 = SizedList(size='n_comp')
adsorption_rate_linear = SizedList(size='n_comp')
adsorption_rate_quadratic = SizedList(size='n_comp', default=0)
adsorption_rate_cubic = SizedList(size='n_comp', default=0)
adsorption_rate_salt = SizedList(size='n_comp', default=0)
adsorption_rate_protein = SizedList(size='n_comp', default=0)
desorption_rate = SizedList(size='n_comp')
desorption_rate_linear = SizedList(size='n_comp', default=0)
desorption_rate_quadratic = SizedList(size='n_comp', default=0)
desorption_rate_cubic = SizedList(size='n_comp', default=0)
desorption_rate_salt = SizedList(size='n_comp', default=0)
desorption_rate_protein = SizedList(size='n_comp', default=0)
characteristic_charge_breaks = DependentlyModulatedUnsignedList(
size='n_comp', is_optional=True
)
characteristic_charge = SizedList(size=('n_pieces', 'n_comp'),)
characteristic_charge_linear = SizedList(size=('n_pieces', 'n_comp'), default=0)
characteristic_charge_quadratic = SizedList(size=('n_pieces', 'n_comp'), default=0)
characteristic_charge_cubic = SizedList(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: 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
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 = SizedList(size='n_comp')
desorption_rate = SizedList(size='n_comp')
capacity = SizedList(size='n_comp')
hic_characteristic = SizedList(size='n_comp')
beta_0 = UnsignedFloat()
beta_1 = UnsignedFloat()
_parameters = [
'adsorption_rate',
'desorption_rate',
'hic_characteristic',
'capacity',
'beta_0',
'beta_1',
]
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 = SizedList(size='n_comp')
desorption_rate = SizedList(size='n_comp')
capacity = SizedList(size='n_comp')
hic_characteristic = SizedList(size='n_comp')
beta_0 = UnsignedFloat()
beta_1 = UnsignedFloat()
_parameters = [
'adsorption_rate',
'desorption_rate',
'hic_characteristic',
'capacity',
'beta_0',
'beta_1',
]
