"""
:meta private:
"""
from __future__ import annotations
from typing import Literal, Optional
from pharmpy.basic import Expr
from pharmpy.model import (
Assignment,
Compartment,
CompartmentalSystem,
CompartmentalSystemBuilder,
Model,
get_and_check_odes,
output,
)
from pharmpy.modeling import get_central_volume_and_clearance
from .error import set_proportional_error_model
from .expressions import _replace_trivial_redefinitions
from .odes import add_individual_parameter, set_first_order_elimination, set_initial_condition
from .parameter_variability import add_iiv
TMDD_TYPE = ('full', 'ib', 'cr', 'crib', 'qss', 'wagner', 'mmapp')
DV_TYPES = ('drug', 'drug_tot', 'target', 'target_tot', 'complex')
[docs]
def set_tmdd(
model: Model,
type: Literal['full', 'ib', 'cr', 'crib', 'qss', 'wagner', 'mmapp'],
dv_types: Optional[
dict[Literal['drug', 'drug_tot', 'target', 'target_tot', 'complex'], int]
] = None,
):
"""Sets target mediated drug disposition
Implemented target mediated drug disposition (TMDD) models are:
- Full model
- Irreversible binding approximation (IB)
- Constant total receptor approximation (CR)
- Irreversible binding and constant total receptor approximation (CR+IB)
- Quasi steady-state approximation (QSS)
- Wagner
- Michaelis-Menten approximation (MMAPP)
Parameters
----------
model : Model
Pharmpy model
type : str
Type of TMDD model
dv_types: dict
Dictionary of DV types for TMDD models with multiple DVs (e.g. dv_types = {'drug' : 1, 'target': 2}).
Default is None which means that all observations are treated as drug observations.
For dv = 1 the only allowed keys are 'drug' and 'drug_tot'. If no DV for drug is specified then (free) drug
will have dv = 1.
Return
------
Model
Pharmpy model object
Examples
--------
>>> from pharmpy.modeling import *
>>> model = load_example_model("pheno")
>>> model = set_tmdd(model, "full")
"""
if dv_types is not None:
_validate_dv_types(dv_types)
uptype = type.upper()
model = _replace_trivial_redefinitions(model)
model = set_first_order_elimination(model)
odes = get_and_check_odes(model)
central = odes.central_compartment
cb = CompartmentalSystemBuilder(odes)
vc, cl = get_central_volume_and_clearance(model)
r_0 = Expr.symbol('R_0')
model = add_individual_parameter(model, r_0.name)
model = add_iiv(model, [r_0], 'exp')
kint = Expr.symbol('KINT')
model = add_individual_parameter(model, kint.name)
y_symbol = _get_y_symbol(model)
if uptype == "FULL":
model, kon, koff, kdeg = _create_parameters(model, ['KON', 'KOFF', 'KDEG'])
target_comp, complex_comp = _create_compartments(cb, ['TARGET', 'COMPLEX'])
ksyn, ksyn_ass = _create_ksyn()
cb.add_flow(target_comp, complex_comp, kon * central.amount / vc)
cb.add_flow(complex_comp, target_comp, koff)
cb.add_flow(target_comp, output, kdeg)
cb.add_flow(complex_comp, output, kint)
cb.set_input(target_comp, ksyn * vc)
cb.set_input(
central, koff * complex_comp.amount - kon * central.amount * target_comp.amount / vc
)
before = model.statements.before_odes + ksyn_ass
after = model.statements.after_odes
elif uptype == "IB":
model, kdeg, kon = _create_parameters(model, ['KDEG', 'KON'])
target_comp, complex_comp = _create_compartments(cb, ['TARGET', 'COMPLEX'])
ksyn, ksyn_ass = _create_ksyn()
cb.add_flow(target_comp, complex_comp, kon * central.amount / vc)
cb.add_flow(target_comp, output, kdeg)
cb.add_flow(complex_comp, output, kint)
cb.set_input(target_comp, ksyn * vc)
cb.set_input(central, -kon * central.amount * target_comp.amount / vc)
before = model.statements.before_odes + ksyn_ass
after = model.statements.after_odes
elif uptype == "CR":
model, kon, koff = _create_parameters(model, ['KON', 'KOFF'])
complex_comp = _create_compartments(cb, ['COMPLEX'])
cb.add_flow(complex_comp, central, koff + kon * central.amount / vc)
cb.add_flow(complex_comp, output, kint)
cb.add_flow(central, complex_comp, kon * r_0)
before = model.statements.before_odes
after = model.statements.after_odes
elif uptype == "CRIB":
model, kon = _create_parameters(model, ['KON'])
complex_comp = _create_compartments(cb, ['COMPLEX'])
cb.add_flow(complex_comp, output, kint)
cb.add_flow(central, complex_comp, kon * r_0)
cb.add_flow(complex_comp, central, kon * central.amount / vc)
before = model.statements.before_odes
after = model.statements.after_odes
elif uptype == "QSS":
model, kdc, kdeg = _create_parameters(model, ['KDC', 'KDEG'])
target_comp = _create_compartments(cb, ['TARGET'])
kd = Expr.symbol('KD')
ksyn, ksyn_ass = _create_ksyn()
kd_ass = Assignment.create(kd, kdc * vc)
lafree_symb = Expr.symbol('LAFREE')
lafree_expr = (
central.amount
- target_comp.amount
- kd
+ ((central.amount - target_comp.amount - kd) ** 2 + 4 * kd * central.amount).sqrt()
) / 2
lafree_ass = Assignment.create(lafree_symb, lafree_expr)
num_peripheral_comp = len(odes.find_peripheral_compartments())
if num_peripheral_comp == 0:
elimination_rate = odes.get_flow(central, output)
cb.remove_flow(central, output)
cb.set_input(
central,
-lafree_symb * elimination_rate
- target_comp.amount * kint * lafree_symb / (kd + lafree_symb),
)
cb.set_input(
target_comp,
ksyn * vc
- kdeg * target_comp.amount
- (kint - kdeg) * target_comp.amount * lafree_symb / (kd + lafree_symb),
)
# FIXME: Should others also have flows?
central = cb.find_compartment('CENTRAL')
cb.add_flow(central, output, lafree_symb * elimination_rate)
lafreef = Expr.symbol("LAFREEF")
lafree_final = Assignment.create(lafreef, lafree_expr)
before = model.statements.before_odes + (ksyn_ass, kd_ass, lafree_ass)
after = lafree_final + model.statements.after_odes
ipred = lafreef / vc
after = after.reassign(y_symbol, ipred)
elif num_peripheral_comp > 0 and num_peripheral_comp <= 2:
peripheral1 = _create_compartments(cb, ['PERIPHERAL1'])
flow_central_peripheral1 = odes.get_flow(central, peripheral1)
if num_peripheral_comp == 2:
peripheral2 = _create_compartments(cb, ['PERIPHERAL2'])
flow_central_peripheral2 = odes.get_flow(central, peripheral2)
elimination_rate = odes.get_flow(central, output)
cb.remove_flow(central, output)
if num_peripheral_comp == 1:
cb.set_input(
central,
-target_comp.amount * kint * lafree_symb / (kd + lafree_symb)
- lafree_symb * flow_central_peripheral1
+ flow_central_peripheral1 * central.amount,
)
cb.set_input(
target_comp,
ksyn * vc
- kdeg * target_comp.amount
- (kint - kdeg) * target_comp.amount * lafree_symb / (kd + lafree_symb),
)
cb.set_input(
peripheral1,
lafree_symb * flow_central_peripheral1
- flow_central_peripheral1 * central.amount,
)
elif num_peripheral_comp == 2:
cb.set_input(
central,
-target_comp.amount * kint * lafree_symb / (kd + lafree_symb)
- lafree_symb * flow_central_peripheral1
- lafree_symb * flow_central_peripheral2
+ flow_central_peripheral2 * central.amount,
)
cb.set_input(
target_comp,
ksyn * vc
- kdeg * target_comp.amount
- (kint - kdeg) * target_comp.amount * lafree_symb / (kd + lafree_symb),
)
cb.set_input(
peripheral1,
lafree_symb * flow_central_peripheral1
- flow_central_peripheral1 * central.amount,
)
cb.set_input(
peripheral2,
lafree_symb * flow_central_peripheral2
- flow_central_peripheral2 * central.amount,
)
central = cb.find_compartment('CENTRAL')
cb.add_flow(central, output, lafree_symb * elimination_rate / central.amount)
lafreef = Expr.symbol("LAFREEF")
lafree_final = Assignment.create(lafreef, lafree_expr)
before = model.statements.before_odes + (ksyn_ass, kd_ass, lafree_ass)
after = lafree_final + model.statements.after_odes
ipred = lafreef / vc
after = after.reassign(y_symbol, ipred)
else:
raise ValueError('More than 2 peripheral compartments are not supported.')
elif uptype == 'WAGNER':
model, km = _create_parameters(model, ['KM'])
kel = odes.get_flow(central, output)
kd = km * vc
rinit = r_0 * vc
rinit_ass = Assignment(Expr.symbol('RINIT'), rinit)
kd_ass = Assignment(Expr.symbol('KD'), km * vc)
lafree_symb = Expr.symbol('LAFREE')
lafree_expr = (
central.amount
- rinit
- kd
+ ((central.amount - rinit - kd) ** 2 + 4 * kd * central.amount).sqrt()
) / 2
lafree_ass = Assignment.create(lafree_symb, lafree_expr)
num_peripheral_comp = len(odes.find_peripheral_compartments())
if num_peripheral_comp == 0:
cb.add_flow(central, output, kel)
cb.set_input(
central,
kint * lafree_symb
- kint * central.amount
- kel * lafree_symb
+ kel * central.amount,
)
elif num_peripheral_comp == 1:
peripheral = _create_compartments(cb, ['PERIPHERAL1'])
kcp = odes.get_flow(central, peripheral)
cb.add_flow(central, output, kel)
cb.set_input(
central,
kint * lafree_symb
- kint * central.amount
- kel * lafree_symb
+ kel * central.amount
- kcp * lafree_symb
+ kcp * central.amount,
)
cb.set_input(peripheral, kcp * lafree_symb - kcp * central.amount)
elif num_peripheral_comp == 2:
peripheral1 = _create_compartments(cb, ['PERIPHERAL1'])
kcp1 = odes.get_flow(central, peripheral1)
peripheral2 = _create_compartments(cb, ['PERIPHERAL2'])
kcp2 = odes.get_flow(central, peripheral2)
cb.add_flow(central, output, kel)
cb.set_input(
central,
kint * lafree_symb
- kint * central.amount
- kel * lafree_symb
+ kel * central.amount
- kcp1 * lafree_symb
- kcp2 * lafree_symb,
)
cb.set_input(peripheral1, kcp1 * lafree_symb - kcp1 * central.amount)
cb.set_input(peripheral2, kcp2 * lafree_symb - kcp2 * central.amount)
lafreef = Expr.symbol("LAFREEF")
lafree_final = Assignment.create(lafreef, lafree_expr)
before = model.statements.before_odes + lafree_ass + kd_ass + rinit_ass
after = lafree_final + model.statements.after_odes
ipred = lafreef / vc
after = after.reassign(y_symbol, ipred)
elif uptype == 'MMAPP':
model, km, kdeg = _create_parameters(model, ['KM', 'KDEG'])
target_comp = _create_compartments(cb, ['TARGET'])
ksyn, ksyn_ass = _create_ksyn()
target_elim = kdeg + (kint - kdeg) * central.amount / vc / (km + central.amount / vc)
cb.add_flow(target_comp, output, target_elim)
elim = cl / vc
cb.add_flow(central, output, elim)
cb.set_input(target_comp, ksyn)
cb.set_input(
central, -target_comp.amount * central.amount * kint / (central.amount / vc + km)
)
before = model.statements.before_odes + ksyn_ass
after = model.statements.after_odes
else:
raise ValueError(f'Unknown TMDD type "{type}".')
model = model.replace(statements=before + CompartmentalSystem(cb) + after)
if uptype not in ('CR', 'CRIB', 'WAGNER', 'MMAPP'):
model = set_initial_condition(model, "TARGET", r_0 * vc)
if uptype == 'MMAPP':
model = set_initial_condition(model, "TARGET", r_0)
# Multiple DVs:
if dv_types is not None:
if uptype in ('FULL', 'IB'):
if 'drug_tot' in dv_types.keys():
new_y = (central.amount + complex_comp.amount) / vc
after = model.statements.after_odes
after = after.reassign(y_symbol, new_y)
model = model.replace(
statements=model.statements.before_odes + model.statements.ode_system + after
)
if 'target' in dv_types.keys():
y_target = Expr.symbol("Y_TARGET")
ytarget = Assignment.create(y_target, target_comp.amount / vc)
dvs = model.dependent_variables.replace(y_target, dv_types['target'])
model = model.replace(
statements=model.statements + ytarget, dependent_variables=dvs
)
if 'complex' in dv_types.keys():
y_complex = Expr.symbol("Y_COMPLEX")
ycomplex = Assignment.create(y_complex, complex_comp.amount / vc)
dvs = model.dependent_variables.replace(y_complex, dv_types['complex'])
model = model.replace(
statements=model.statements + ycomplex, dependent_variables=dvs
)
if 'target_tot' in dv_types.keys():
y_target_tot = Expr.symbol("Y_TOTTARGET")
ytargettot = Assignment.create(
y_target_tot, (target_comp.amount + complex_comp.amount) / vc
)
dvs = model.dependent_variables.replace(y_target_tot, dv_types['target_tot'])
model = model.replace(
statements=model.statements + ytargettot, dependent_variables=dvs
)
elif uptype == 'QSS':
if 'drug_tot' in dv_types.keys():
new_y = central.amount / vc
after = model.statements.after_odes
after = after.reassign(y_symbol, new_y)
model = model.replace(
statements=model.statements.before_odes + model.statements.ode_system + after
)
if 'target' in dv_types.keys():
y_target = Expr.symbol("Y_TARGET")
ytarget = Assignment.create(
y_target, (target_comp.amount - central.amount + lafreef) / vc
)
dvs = model.dependent_variables.replace(y_target, dv_types['target'])
model = model.replace(
statements=model.statements + ytarget, dependent_variables=dvs
)
if 'complex' in dv_types.keys():
y_complex = Expr.symbol("Y_COMPLEX")
ycomplex = Assignment.create(y_complex, (central.amount - lafreef) / vc)
dvs = model.dependent_variables.replace(y_complex, dv_types['complex'])
model = model.replace(
statements=model.statements + ycomplex, dependent_variables=dvs
)
if 'target_tot' in dv_types.keys():
y_target_tot = Expr.symbol("Y_TOTTARGET")
ytargettot = Assignment.create(y_target_tot, target_comp.amount / vc)
dvs = model.dependent_variables.replace(y_target_tot, dv_types['target_tot'])
model = model.replace(
statements=model.statements + ytargettot, dependent_variables=dvs
)
elif uptype == 'MMAPP':
if 'target' in dv_types.keys():
y_target = Expr.symbol("Y_TARGET")
ytarget = Assignment.create(y_target, target_comp.amount / vc)
dvs = model.dependent_variables.replace(y_target, dv_types['target'])
model = model.replace(
statements=model.statements + ytarget, dependent_variables=dvs
)
if 'target_tot' in dv_types.keys():
y_target_tot = Expr.symbol("Y_TOTTARGET")
ytargettot = Assignment.create(y_target_tot, target_comp.amount / vc)
dvs = model.dependent_variables.replace(y_target_tot, dv_types['target_tot'])
model = model.replace(
statements=model.statements + ytargettot, dependent_variables=dvs
)
elif uptype in ('CR', 'CRIB'):
if 'drug_tot' in dv_types.keys():
new_y = (central.amount + complex_comp.amount) / vc
after = model.statements.after_odes
after = after.reassign(y_symbol, new_y)
model = model.replace(
statements=model.statements.before_odes + model.statements.ode_system + after
)
if 'complex' in dv_types.keys():
y_complex = Expr.symbol("Y_COMPLEX")
ycomplex = Assignment.create(y_complex, complex_comp.amount / vc)
dvs = model.dependent_variables.replace(y_complex, dv_types['complex'])
model = model.replace(
statements=model.statements + ycomplex, dependent_variables=dvs
)
elif uptype == 'WAGNER':
if 'drug_tot' in dv_types.keys():
new_y = central.amount / vc
after = model.statements.after_odes
after = after.reassign(y_symbol, new_y)
model = model.replace(
statements=model.statements.before_odes + model.statements.ode_system + after
)
if 'complex' in dv_types.keys():
y_complex = Expr.symbol("Y_COMPLEX")
ycomplex = Assignment.create(y_complex, (central.amount - lafreef) / vc)
dvs = model.dependent_variables.replace(y_complex, dv_types['complex'])
model = model.replace(
statements=model.statements + ycomplex, dependent_variables=dvs
)
# Add proportional error model
if Expr.symbol('Y_TARGET') in list(model.dependent_variables):
model = set_proportional_error_model(model, dv=dv_types['target'])
if Expr.symbol('Y_COMPLEX') in list(model.dependent_variables):
model = set_proportional_error_model(model, dv=dv_types['complex'])
if Expr.symbol('Y') in list(model.dependent_variables) and 'drug_tot' in dv_types.keys():
model = set_proportional_error_model(model, dv=dv_types['drug_tot'])
if Expr.symbol('Y_TOTTARGET') in list(model.dependent_variables):
model = set_proportional_error_model(model, dv=dv_types['target_tot'])
if model.dataset is not None:
try:
dvid = model.datainfo.typeix['dvid']
except IndexError:
# FIXME: Should be enough to look in datainfo
if 'DVID' in model.dataset.columns:
dvid = 'DVID'
else:
raise ValueError("DVID column in dataset is needed when using dv_types.")
dvs = [dv for dv in model.dependent_variables.values()]
model = model.replace(dataset=model.dataset.query(f'{dvid} in @dvs'))
return model.update_source()
def _create_parameters(model, names):
symbs = []
for name in names:
symb = Expr.symbol(name)
symbs.append(symb)
model = add_individual_parameter(model, symb.name)
return model, *symbs
def _create_compartments(cb, names):
comps = []
for name in names:
comp = Compartment.create(name=name)
comps.append(comp)
cb.add_compartment(comp)
if len(comps) == 1:
return comps[0]
else:
return comps
def _create_ksyn():
ksyn = Expr.symbol('KSYN')
ksyn_ass = Assignment.create(ksyn, Expr.symbol("R_0") * Expr.symbol("KDEG"))
return ksyn, ksyn_ass
def _validate_dv_types(dv_types):
# Make sure that values are unique
assert len(dv_types.values()) == len(set(dv_types.values()))
# Validate keys
for key, value in dv_types.items():
if key not in ['drug', 'target', 'complex', 'drug_tot', 'target_tot']:
raise ValueError(
f'Invalid dv_types key "{key}". Allowed keys are:'
f' "drug", "target", "complex", "drug_tot" and "target_tot".'
)
if key not in ['drug', 'drug_tot'] and value == 1:
raise ValueError('Only drug can have DVID = 1. Please choose another DVID.')
def _get_y_symbol(model):
t = Expr.symbol("t")
y_statement = model.statements.find_assignment("Y")
if t in y_statement.free_symbols:
return y_statement.symbol
else:
sset = model.statements.direct_dependencies(y_statement)
for s in sset:
if Expr.symbol("t") in s.free_symbols:
return s.symbol
