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test_macros.py
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from pysb.testing import *
from pysb.core import *
import numpy as np
from pysb.pkpd.macros import *
@with_model
def test_drug_monomer():
drug_monomer()
assert len(model.monomers) == 1
assert model.monomers[0].name == "Drug"
drug_monomer("D2")
assert len(model.monomers) == 2
assert model.monomers[-1].name == "D2"
@with_model
def test_one_compartment():
one_compartment()
assert len(model.compartments) == 1
assert model.compartments[0].name == "CENTRAL"
assert np.isclose(model.compartments[0].size.value, 1.0)
assert len(model.parameters) == 1
one_compartment("C2", 2.0)
assert len(model.compartments) == 2
assert model.compartments[-1].name == "C2"
assert np.isclose(model.compartments[-1].size.value, 2.0)
assert len(model.parameters) == 2
@with_model
def test_two_compartments():
two_compartments()
assert len(model.compartments) == 2
assert model.compartments[0].name == "CENTRAL"
assert model.compartments[1].name == "PERIPHERAL"
assert np.isclose(model.compartments[0].size.value, 1.0)
assert np.isclose(model.compartments[1].size.value, 1.0)
assert len(model.parameters) == 2
two_compartments("C2", 2.0, "P2", 0.1)
assert len(model.compartments) == 4
assert model.compartments[2].name == "C2"
assert model.compartments[3].name == "P2"
assert np.isclose(model.compartments[2].size.value, 2.0)
assert np.isclose(model.compartments[3].size.value, 0.1)
assert len(model.parameters) == 4
@with_model
def test_three_compartments():
three_compartments()
assert len(model.compartments) == 3
assert model.compartments[0].name == "CENTRAL"
assert model.compartments[1].name == "PERIPHERAL"
assert model.compartments[2].name == "DEEPPERIPHERAL"
assert np.isclose(model.compartments[0].size.value, 1.0)
assert np.isclose(model.compartments[1].size.value, 1.0)
assert np.isclose(model.compartments[2].size.value, 1.0)
assert len(model.parameters) == 3
three_compartments("C2", 2.0, "P2", 0.1, "DP2", 0.4)
assert len(model.compartments) == 6
assert model.compartments[3].name == "C2"
assert model.compartments[4].name == "P2"
assert model.compartments[5].name == "DP2"
assert np.isclose(model.compartments[3].size.value, 2.0)
assert np.isclose(model.compartments[4].size.value, 0.1)
assert np.isclose(model.compartments[5].size.value, 0.4)
assert len(model.parameters) == 6
def base_components():
one_compartment()
drug_monomer()
return
# ---- PK Macros ----
@with_model
def test_eliminate():
base_components()
eliminate(Drug, CENTRAL, kel=0.1)
assert len(model.parameters) == 2
assert len(model.rules) == 1
@with_model
def test_eliminate_mm():
base_components()
eliminate_mm(Drug, CENTRAL, vmax=0.1, km=100.0)
assert len(model.parameters) == 3
assert len(model.rules) == 1
assert len(model.expressions) == 1
@with_model
def test_clearance():
base_components()
clearance(Drug, CENTRAL, cl=10.0)
assert len(model.parameters) == 2
assert len(model.rules) == 1
assert len(model.expressions) == 1
@with_model
def test_distribute():
base_components()
one_compartment("PERIPHERAL")
distribute(Drug, CENTRAL, PERIPHERAL, klist=[0.1, 0.05])
assert len(model.parameters) == 4
assert len(model.rules) == 1
assert len(model.expressions) == 0
@with_model
def test_transfer():
base_components()
one_compartment("PERIPHERAL")
transfer(Drug, CENTRAL, PERIPHERAL, k=0.01)
assert len(model.parameters) == 3
assert len(model.rules) == 1
assert len(model.expressions) == 0
# ---- PD Macros ----
@with_model
def test_emax():
base_components()
emax(Drug, CENTRAL, emax=10.0, ec50=100.0)
assert len(model.parameters) == 3
assert len(model.rules) == 0
assert len(model.expressions) == 1
assert len(model.observables) == 1
@with_model
def test_sigmoidal_emax():
base_components()
sigmoidal_emax(Drug, CENTRAL, emax=10.0, ec50=100.0, n=2.0)
assert len(model.parameters) == 4
assert len(model.rules) == 0
assert len(model.expressions) == 1
assert len(model.observables) == 1
@with_model
def test_linear_effect():
base_components()
linear_effect(Drug, CENTRAL, slope=0.1, intercept=1.0)
assert len(model.parameters) == 3
assert len(model.rules) == 0
assert len(model.expressions) == 1
assert len(model.observables) == 1
@with_model
def test_loglinear_effect():
base_components()
loglinear_effect(Drug, CENTRAL, slope=0.1, intercept=1.0, base=2)
assert len(model.parameters) == 3
assert len(model.rules) == 0
assert len(model.expressions) == 1
assert len(model.observables) == 1
@with_model
def test_fixed_effect():
base_components()
fixed_effect(Drug, CENTRAL, e_fixed=1.0, c_threshold=24.6)
assert len(model.parameters) == 3
assert len(model.rules) == 0
assert len(model.expressions) == 1
assert len(model.observables) == 1
# ---- Dose Macros ----
@with_model
def test_dose_bolus():
base_components()
dose_bolus(Drug, CENTRAL, dose=100.0)
assert len(model.parameters) == 2
assert len(model.rules) == 0
assert len(model.expressions) == 1
assert len(model.initials) == 1
@with_model
def test_dose_infusion():
base_components()
dose_infusion(Drug, CENTRAL, dose=2.0)
assert len(model.parameters) == 2
assert len(model.rules) == 1
assert len(model.expressions) == 1
assert len(model.initials) == 0
@with_model
def test_dose_absorbed():
base_components()
dose_absorbed(Drug, CENTRAL, dose=10.0, ka=1e-1, f=0.78)
assert len(model.parameters) == 4
assert len(model.rules) == 1
assert len(model.expressions) == 2
assert len(model.initials) == 1
assert len(model.monomers) == 2
if __name__ == "__main__":
test_drug_monomer()
test_one_compartment()
test_two_compartments()
test_three_compartments()
test_eliminate()
test_eliminate_mm()
test_clearance()
test_distribute()
test_transfer()
test_emax()
test_sigmoidal_emax()
test_linear_effect()
test_loglinear_effect()
test_fixed_effect()
test_dose_bolus()
test_dose_infusion()
test_dose_absorbed()