public override void GlobalContext()
{
base.GlobalContext();
_compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
_cloneManager = IoC.Resolve <ICloneManager>();
_enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
_transporterFactory = IoC.Resolve <IIndividualTransporterFactory>();
_modelPropertiesTask = IoC.Resolve <IModelPropertiesTask>();
_modelConfigurationRepository = IoC.Resolve <IModelConfigurationRepository>();
_compound = DomainFactoryForSpecs.CreateStandardCompound();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_enzyme = _enzymeFactory.AddMoleculeTo(_individual, "CYP").DowncastTo <IndividualEnzyme>();
_allExpressionParameters = _individual.AllExpressionParametersFor(_enzyme);
_allExpressionParameters[CoreConstants.Compartment.PLASMA].Value = _relExpPls;
_allExpressionParameters[CoreConstants.Compartment.BLOOD_CELLS].Value = _relExpBloodCells;
_allExpressionParameters[CoreConstants.Compartment.VASCULAR_ENDOTHELIUM].Value = _relExpVascEndo;
_hct = _individual.Organism.Parameter(CoreConstants.Parameters.HCT).Value;
_metabolizationProcess = _cloneManager.Clone(_compoundProcessRepository
.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>());
_metabolizationProcess.Name = "My Partial Process";
_metabolizationProcess.Parameter(ConverterConstants.Parameters.CLspec).Value = 15;
_compound.AddProcess(_metabolizationProcess);
_simulationRunOptions = new SimulationRunOptions {
RaiseEvents = false
};
}
public void should_have_normalized_the_expression()
{
var enzyme = _individual.MoleculeByName <IndividualEnzyme>("E1_Intracellular_Endosomal");
var allExpressionParameters = _individual.AllExpressionParametersFor(enzyme);
allExpressionParameters[CoreConstants.Compartment.VASCULAR_ENDOTHELIUM].Value.ShouldBeEqualTo(1);
allExpressionParameters[CoreConstants.Compartment.PLASMA].Value.ShouldBeEqualTo(2 / 3.0);
allExpressionParameters[CoreConstants.Compartment.BLOOD_CELLS].Value.ShouldBeEqualTo(1 / 3.0);
}
private void verifyIndividual(Individual individual)
{
individual.AllMolecules <IndividualProtein>().Each(m =>
{
m.Localization.ShouldNotBeEqualTo(Localization.None);
//Should have created parameters in most compartments. About 30+
var allExpressionParameters = individual.AllExpressionParametersFor(m);
allExpressionParameters.Count.ShouldBeGreaterThan(30);
});
}
protected IndividualEnzyme AddEnzymeTo(Individual individual, string enzymeName)
{
var enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
var enzyme = enzymeFactory.AddMoleculeTo(_individual, enzymeName).DowncastTo <IndividualEnzyme>();
var allExpressionParameters = _individual.AllExpressionParametersFor(enzyme);
allExpressionParameters[CoreConstants.Compartment.PERICENTRAL].Value = 1;
allExpressionParameters[CoreConstants.Compartment.PERIPORTAL].Value = 1;
individual.AddMolecule(enzyme);
return(enzyme);
}