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Merged
DavAug merged 1 commit into from
Oct 18, 2025
Merged

Add 2 compartment PK model #279

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41 changes: 39 additions & 2 deletions chi/library/_model_library_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def erlotinib_tumour_growth_inhibition_model(self):

return chi.PKPDModel(self._path + file_name)

def one_compartment_pk_model(self):
def one_compartment_pk_model(self, elimination_rate=True):
r"""
Returns an instantiation of a 1-compartment PK model.

Expand All @@ -62,9 +62,46 @@ def one_compartment_pk_model(self):
The drug may be either directly administered to :math:`A` or indirectly
through a dosing compartment.

:param bool elimination_rate: If True, the model uses the elimination
rate :math:`k_e` as a parameter. If False, the model uses the
clearance :math:`CL` as a parameter, which is related to the
elimination rate by :math:`CL = k_e V`.

:rtype: chi.PKPDModel
"""
file_name = 'pk_one_comp_clearance.xml'
if elimination_rate:
file_name = 'pk_one_comp.xml'
model = chi.PKPDModel(self._path + file_name)
model.set_outputs(['central.drug_concentration'])

return model

def two_compartment_pk_model(self):
r"""
Returns an instantiation of a 2-compartment PK model.

In this model the distribution of the drug is modelled by twp
compartments: 1. the central compartment; and 2. the peripheral
compartment. The drug transtions between the two compartments at the
inter-compartment clearance rate :math:`q` and is eliminated from the
central compartment at the clearance rate :math:`k_{cl}`.

.. math ::
\frac{\text{d}a_c}{\text{d}t} = -k_{cl} c_c - q c_c + q c_p
\quad \frac{\text{d}a_p}{\text{d}t} = q c_c - q c_p,

where :math:`a_c` denotes the drug amount in the central compartment
and :math:`a_p` the drug amount in the peripheral compartment. The
concentrations :math:`c_c` and :math:`c_p` are given by
:math:`c_c = \frac{a_c}{v_c}` and :math:`c_p = \frac{a_p}{v_p}`, where
:math:`v_c` and :math:`v_p` denote the effective volumes of
distribution of the drug in the compartments. `k_{cl}` and `q` denote
the clearance and inter-compartment clearance rates, respectively.

:rtype: chi.PKPDModel
"""
file_name = 'pk_one_comp.xml'
file_name = 'pk_two_comp_clearance.xml'
model = chi.PKPDModel(self._path + file_name)
model.set_outputs(['central.drug_concentration'])

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54 changes: 54 additions & 0 deletions chi/library/model_library/pk_one_comp_clearance.xml
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@@ -0,0 +1,54 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model id="one_compartment_pk_model" timeUnits="hour">

<listOfUnitDefinitions>
<unitDefinition id="hour">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="3600"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="liter_per_hour">
<listOfUnits>
<unit kind="liter" exponent="1" scale="0" multiplier="1"/>
<unit kind="second" exponent="-1" scale="0" multiplier="3600"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="mg">
<listOfUnits>
<unit kind="gram" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>

<listOfCompartments>
<compartment id="central" name="central" size="1" units="liter"/>
</listOfCompartments>

<listOfSpecies>
<species id="drug" name="drug" compartment="central" initialAmount="0" hasSubstanceUnits="false" substanceUnits="mg"/>
</listOfSpecies>

<listOfParameters>
<parameter id="clearance" value="1" constant="true" units="liter_per_hour"/>
</listOfParameters>

<listOfReactions>
<reaction id="central_reaction" name="central_reaction" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="drug"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> clearance </ci>
<ci> drug </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>

</model>
</sbml>
93 changes: 93 additions & 0 deletions chi/library/model_library/pk_two_comp_clearance.xml
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@@ -0,0 +1,93 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model id="two_compartment_pk_model" timeUnits="hour">

<listOfUnitDefinitions>
<unitDefinition id="hour">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="3600"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="liter_per_hour">
<listOfUnits>
<unit kind="liter" exponent="1" scale="0" multiplier="1"/>
<unit kind="second" exponent="-1" scale="0" multiplier="3600"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="mg">
<listOfUnits>
<unit kind="gram" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>

<listOfCompartments>
<compartment id="central" name="central" size="1" units="liter"/>
<compartment id="peripheral" name="peripheral" size="1" units="liter"/>
</listOfCompartments>

<listOfSpecies>
<species id="drug" name="drug" compartment="central" initialAmount="0" hasSubstanceUnits="false" substanceUnits="mg"/>
<species id="drug_peripheral" name="drug_peripheral" compartment="peripheral" initialAmount="0" hasSubstanceUnits="false" substanceUnits="mg"/>
</listOfSpecies>

<listOfParameters>
<parameter id="clearance" value="1" constant="true" units="liter_per_hour"/>
<parameter id="inter_compartment_clearance" value="1" constant="true" units="liter_per_hour"/>
</listOfParameters>

<listOfReactions>
<reaction id="clearance_reaction" name="clearance_reaction" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="drug"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> clearance </ci>
<ci> drug </ci>
</apply>
</math>
</kineticLaw>
</reaction>

<reaction id="transition_to_peripheral_compartment" name="transition_to_peripheral_compartment" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="drug"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="drug_peripheral"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> inter_compartment_clearance </ci>
<ci> drug </ci>
</apply>
</math>
</kineticLaw>
</reaction>

<reaction id="transition_to_central_compartment" name="transition_to_central_compartment" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="drug_peripheral"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="drug"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> inter_compartment_clearance </ci>
<ci> drug_peripheral </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>

</model>
</sbml>
9 changes: 9 additions & 0 deletions chi/tests/test_model_library_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,15 @@ def test_existence_one_compartment_pk_model(self):
model = self.model_library.one_compartment_pk_model()
self.assertIsInstance(model, chi.PKPDModel)

def test_existence_one_compartment_pk_model_clearance(self):
model = self.model_library.one_compartment_pk_model(
elimination_rate=False)
self.assertIsInstance(model, chi.PKPDModel)

def test_existence_two_compartment_pk_model(self):
model = self.model_library.two_compartment_pk_model()
self.assertIsInstance(model, chi.PKPDModel)


class TestErlotinibTumourGrowthInhibitionModel(unittest.TestCase):
"""
Expand Down