Source code for wholecell.tests.utils.test_modular_fba

#!/usr/bin/env python

import unittest

from wholecell.utils.modular_fba import FluxBalanceAnalysis

# Silence Sphinx autodoc warning
unittest.TestCase.__module__ = "unittest"


# TODO: test all solvers

_testStandard = dict(
    reactionStoich={
        "A to B": {"A": -1, "B": +1},
        "2B to C": {"B": -2, "C": +1},
        "A + D to E": {"A": -1, "D": -1, "E": +1},
    },
    externalExchangedMolecules=["A", "D"],
    objective={
        "B": 10,
        "C": 10,
        "E": 20,
    },
)

_testTargetMolecules = dict(
    reactionStoich={
        "A to B": {"A": -1, "B": +1},
        "B to A": {"A": +1, "B": -1},
        "2B to C": {"B": -2, "C": +1},
        "C to 2B": {"B": +2, "C": -1},
        "A + D to E": {"A": -1, "D": -1, "E": +1},
        "E to A + D": {"A": +1, "D": +1, "E": -1},
    },
    externalExchangedMolecules=["A", "D"],
    objective={
        "B": 10,
        "C": 10,
        "E": 20,
    },
    objectiveType="homeostatic",
)




class Test_FluxBalanceAnalysis(unittest.TestCase):


    @classmethod
    def setUpClass(cls):
        pass




    @classmethod
    def tearDownClass(cls):
        pass




    def setUp(self):
        pass




    def tearDown(self):
        pass


    def test_instantiation(self):
        fba = FluxBalanceAnalysis(**_testStandard)
        assert fba is not None

    def test_standard_IDs(self):
        fba = FluxBalanceAnalysis(**_testStandard)

        self.assertEqual(set(fba.getExternalMoleculeIDs()), {"A", "D"})

        self.assertEqual(set(fba.getOutputMoleculeIDs()), {"B", "C", "E"})

    def test_standard_noInput(self):
        fba = FluxBalanceAnalysis(**_testStandard)

        self.assertEqual(fba.getBiomassReactionFlux(), 0)

        for moleculeID, change in zip(
            fba.getOutputMoleculeIDs(), fba.getOutputMoleculeLevelsChange()
        ):
            if moleculeID == "B":
                self.assertAlmostEqual(0, change)

            elif moleculeID == "C":
                self.assertAlmostEqual(0, change)

            elif moleculeID == "E":
                self.assertAlmostEqual(0, change)

    def test_standard(self):
        fba = FluxBalanceAnalysis(**_testStandard)

        externalMoleculeLevels = {"A": 50, "D": 20}

        fba.setExternalMoleculeLevels(
            [
                externalMoleculeLevels[moleculeID]
                for moleculeID in fba.getExternalMoleculeIDs()
            ]
        )

        self.assertEqual(fba.getBiomassReactionFlux(), 1.0)

        for moleculeID, change in zip(
            fba.getOutputMoleculeIDs(), fba.getOutputMoleculeLevelsChange()
        ):
            if moleculeID == "B":
                self.assertAlmostEqual(10, change)

            elif moleculeID == "C":
                self.assertAlmostEqual(10, change)

            elif moleculeID == "E":
                self.assertAlmostEqual(20, change)

    def test_homeostatic_noInitial(self):
        fba = FluxBalanceAnalysis(**_testTargetMolecules)

        externalMoleculeLevels = {"A": 50, "D": 20}

        fba.setExternalMoleculeLevels(
            [
                externalMoleculeLevels[moleculeID]
                for moleculeID in fba.getExternalMoleculeIDs()
            ]
        )

        internalMoleculeLevels = {
            "B": 0,
            "C": 0,
            "E": 0,
        }

        fba.setInternalMoleculeLevels(
            [
                internalMoleculeLevels[moleculeID]
                for moleculeID in fba.getInternalMoleculeIDs()
            ]
        )

        for moleculeID, change in zip(
            fba.getOutputMoleculeIDs(), fba.getOutputMoleculeLevelsChange()
        ):
            if moleculeID == "B":
                self.assertAlmostEqual(10, change)

            elif moleculeID == "C":
                self.assertAlmostEqual(10, change)

            elif moleculeID == "E":
                self.assertAlmostEqual(20, change)

    def test_homeostatic_atObjective(self):
        fba = FluxBalanceAnalysis(**_testTargetMolecules)

        externalMoleculeLevels = {"A": 50, "D": 20}

        fba.setExternalMoleculeLevels(
            [
                externalMoleculeLevels[moleculeID]
                for moleculeID in fba.getExternalMoleculeIDs()
            ]
        )

        internalMoleculeLevels = {
            "B": 10,
            "C": 10,
            "E": 20,
        }

        fba.setInternalMoleculeLevels(
            [
                internalMoleculeLevels[moleculeID]
                for moleculeID in fba.getInternalMoleculeIDs()
            ]
        )

        for moleculeID, change in zip(
            fba.getOutputMoleculeIDs(), fba.getOutputMoleculeLevelsChange()
        ):
            if moleculeID == "B":
                self.assertAlmostEqual(0, change)

            elif moleculeID == "C":
                self.assertAlmostEqual(0, change)

            elif moleculeID == "E":
                self.assertAlmostEqual(0, change)

    def test_homeostatic_belowObjective(self):
        fba = FluxBalanceAnalysis(**_testTargetMolecules)

        externalMoleculeLevels = {"A": 50, "D": 20}

        fba.setExternalMoleculeLevels(
            [
                externalMoleculeLevels[moleculeID]
                for moleculeID in fba.getExternalMoleculeIDs()
            ]
        )

        internalMoleculeLevels = {
            "B": 5,
            "C": 5,
            "E": 10,
        }

        fba.setInternalMoleculeLevels(
            [
                internalMoleculeLevels[moleculeID]
                for moleculeID in fba.getInternalMoleculeIDs()
            ]
        )

        for moleculeID, change in zip(
            fba.getOutputMoleculeIDs(), fba.getOutputMoleculeLevelsChange()
        ):
            if moleculeID == "B":
                self.assertAlmostEqual(5, change)

            elif moleculeID == "C":
                self.assertAlmostEqual(5, change)

            elif moleculeID == "E":
                self.assertAlmostEqual(10, change)

    def test_homeostatic_singleBelowObjective(self):
        fba = FluxBalanceAnalysis(**_testTargetMolecules)

        externalMoleculeLevels = {"A": 50, "D": 20}

        fba.setExternalMoleculeLevels(
            [
                externalMoleculeLevels[moleculeID]
                for moleculeID in fba.getExternalMoleculeIDs()
            ]
        )

        internalMoleculeLevels = {
            "B": 5,
            "C": 10,
            "E": 20,
        }

        fba.setInternalMoleculeLevels(
            [
                internalMoleculeLevels[moleculeID]
                for moleculeID in fba.getInternalMoleculeIDs()
            ]
        )

        for moleculeID, change in zip(
            fba.getOutputMoleculeIDs(), fba.getOutputMoleculeLevelsChange()
        ):
            if moleculeID == "B":
                self.assertAlmostEqual(5, change)

            elif moleculeID == "C":
                self.assertAlmostEqual(0, change)

            elif moleculeID == "E":
                self.assertAlmostEqual(0, change)

    def test_homeostatic_singleAboveObjective(self):
        fba = FluxBalanceAnalysis(**_testTargetMolecules)

        externalMoleculeLevels = {"A": 50, "D": 20}

        fba.setExternalMoleculeLevels(
            [
                externalMoleculeLevels[moleculeID]
                for moleculeID in fba.getExternalMoleculeIDs()
            ]
        )

        internalMoleculeLevels = {
            "B": 15,
            "C": 10,
            "E": 20,
        }

        fba.setInternalMoleculeLevels(
            [
                internalMoleculeLevels[moleculeID]
                for moleculeID in fba.getInternalMoleculeIDs()
            ]
        )

        for moleculeID, change in zip(
            fba.getOutputMoleculeIDs(), fba.getOutputMoleculeLevelsChange()
        ):
            if moleculeID == "B":
                self.assertAlmostEqual(-5, change)

            elif moleculeID == "C":
                self.assertAlmostEqual(0, change)

            elif moleculeID == "E":
                self.assertAlmostEqual(0, change)



# TODO: tests for enzymes
# TODO: tests for mass accumulation
# TODO: tests for flexible FBA
# TODO: tests for exceptions