protected override void Context()
{
base.Context();
_simulation = A.Fake <Simulation>();
_mixedInhibition = new InhibitionProcess {
InteractionType = InteractionType.MixedInhibition
}.WithName("MixedInhibition");
_competitiveInhibition = new InhibitionProcess {
InteractionType = InteractionType.CompetitiveInhibition
}.WithName("CompetitiveInhibition");
_compound1 = new Compound().WithName("Compound1");
_compound2 = new Compound().WithName("Compound2");
_compound2.AddProcess(_mixedInhibition);
_compound2.AddProcess(_competitiveInhibition);
_interactionProperties = new InteractionProperties();
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound1, _compound2 });
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _mixedInhibition.Name, CompoundName = _compound2.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _competitiveInhibition.Name, CompoundName = _compound2.Name
});
}
protected override void Context()
{
_simulation = A.Fake <Simulation>();
_mixedInhibition1 = new InhibitionProcess {
InteractionType = InteractionType.MixedInhibition
}.WithName("MixedInhibition1");
_mixedInhibition2 = new InhibitionProcess {
InteractionType = InteractionType.MixedInhibition
}.WithName("MixedInhibition2");
_compound1 = new Compound().WithName("Compound1");
_compound2 = new Compound().WithName("Compound2");
_compound2.AddProcess(_mixedInhibition1);
_compound2.AddProcess(_mixedInhibition2);
_interactionProperties = new InteractionProperties();
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound1, _compound2 });
sut = new MixedInhibitionKineticUpdaterSpecification(new ObjectPathFactoryForSpecs(), A.Fake <IDimensionRepository>(), new InteractionTask());
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _mixedInhibition1.Name, CompoundName = _compound2.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _mixedInhibition2.Name, CompoundName = _compound2.Name
});
}
protected override void Context()
{
_formulaCache = A.Fake <IFormulaCache>();
_repository = A.Fake <IRepository <IInteractionKineticUpdaterSpecification> >();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
A.CallTo(() => _objectBaseFactory.Create <ExplicitFormula>()).ReturnsLazily(x => new ExplicitFormula());
A.CallTo(() => _repository.All()).Returns(_allKineticUpdaterSpecifications);
sut = new InteractionKineticUpdater(_repository, _objectBaseFactory);
_reaction = new ReactionBuilder();
_transporterMoleculeContainer = new TransporterMoleculeContainer();
_simulation = A.Fake <Simulation>();
_interactionProperties = new InteractionProperties();
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _enzymeName, ProcessName = _processName
});
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
_kmFactor = new PKSimParameter().WithName(CoreConstants.Parameter.KM_INTERACTION_FACTOR).WithFormula(new ExplicitFormula("1"));
_vmaxFactor = new PKSimParameter().WithName(CoreConstants.Parameter.KCAT_INTERACTION_FACTOR).WithFormula(new ExplicitFormula("1"));
_reaction.Add(_kmFactor);
_reaction.Add(_vmaxFactor);
_transporterMoleculeContainer.Add(_kmFactor);
_transporterMoleculeContainer.Add(_vmaxFactor);
}
protected override void Context()
{
_simulation = A.Fake <Simulation>();
_irreversibleInhibition1 = new InhibitionProcess {
InteractionType = InteractionType.IrreversibleInhibition
}.WithName("IrreversibleInhibition1");
_irreversibleInhibition2 = new InhibitionProcess {
InteractionType = InteractionType.IrreversibleInhibition
}.WithName("IrreversibleInhibition2");
_uncompetitiveInhibition = new InhibitionProcess {
InteractionType = InteractionType.UncompetitiveInhibition
}.WithName("UncompetitiveInhibition");
_compound1 = new Compound().WithName("Compound1");
_compound1.AddProcess(_irreversibleInhibition1);
_compound1.AddProcess(_uncompetitiveInhibition);
_compound2 = new Compound().WithName("Compound2");
_compound2.AddProcess(_irreversibleInhibition2);
_interactionProperties = new InteractionProperties();
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound1, _compound2 });
_objectPathFactory = new ObjectPathFactoryForSpecs();
_dimensionRepository = A.Fake <IDimensionRepository>();
_interactionTask = new InteractionTask();
sut = new IrreversibleInhibitionKineticUpdaterSpecification(_objectPathFactory, _dimensionRepository, _interactionTask);
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _irreversibleInhibition1.Name, CompoundName = _compound1.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _irreversibleInhibition2.Name, CompoundName = _compound2.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _uncompetitiveInhibition.Name, CompoundName = _compound2.Name
});
}
protected override void Context()
{
base.Context();
_interactionProperties = new InteractionProperties();
var inhibitionProcess = new InhibitionProcess {
InteractionType = InteractionType.CompetitiveInhibition
}.WithName("Proc");
var interaction = new InteractionSelection {
CompoundName = _compound.Name, ProcessName = inhibitionProcess.Name
};
_compound.AddProcess(inhibitionProcess);
_interactionProperties.AddInteraction(interaction);
_compoundProperties = new CompoundProperties();
}
protected override void Context()
{
base.Context();
_moleculeMappable = new IndividualEnzyme().WithName("MoleculeMapped");
_moleculeAlreadySelected = new IndividualEnzyme().WithName("MoleculeAlreadySelected");
_moleculeNotMapped = new IndividualEnzyme().WithName("MoleculeNotMapped");
_inhibitionProcess1 = new InhibitionProcess().WithName("InhibitionProcess1");
_inhibitionProcess2 = new InhibitionProcess().WithName("InhibitionProcess2");
_inductionProcess1 = new InductionProcess().WithName("InductionProcess1");
_inhibitionProcess3 = new InhibitionProcess().WithName("InhibitionProcess3");
_individual.AddMolecule(_moleculeNotMapped);
_individual.AddMolecule(_moleculeMappable);
_individual.AddMolecule(_moleculeAlreadySelected);
_compound.AddProcess(_inhibitionProcess1);
_compound2 = new Compound().WithName("Comp2");
_compound2.AddProcess(_inhibitionProcess2);
_inhibitionProcess2.MoleculeName = _moleculeMappable.Name;
_compound2.AddProcess(_inhibitionProcess3);
_inhibitionProcess3.MoleculeName = _moleculeMappable.Name;
_compound2.AddProcess(_inductionProcess1);
_inductionProcess1.MoleculeName = _moleculeMappable.Name;
var interactionProperties = new InteractionProperties();
interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeAlreadySelected.Name, ProcessName = _inhibitionProcess1.Name, CompoundName = _compound.Name
});
A.CallTo(() => _simulation.InteractionProperties).Returns(interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound, _compound2 });
}