protected override void Context()
{
_project = new PKSimProject();
_projectRetriever = A.Fake <IProjectRetriever>();
A.CallTo(() => _projectRetriever.CurrentProject).Returns(_project);
_compound1 = A.Fake <Compound>();
_compound1.IsLoaded = false;
_compound2 = new Compound {
IsLoaded = true
};
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "A", Name = "P1"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "C", Name = "P2"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "B", Name = "P3"
});
_individual1 = A.Fake <Individual>();
_individual1.IsLoaded = false;
_individual2 = new Individual {
IsLoaded = true
};
_individual2.AddMolecule(new IndividualEnzyme().WithName("B"));
_individual2.AddMolecule(new IndividualEnzyme().WithName("D"));
_project.AddBuildingBlock(_compound1);
_project.AddBuildingBlock(_compound2);
_project.AddBuildingBlock(_individual1);
_project.AddBuildingBlock(_individual2);
sut = new UsedMoleculeRepository(_projectRetriever);
}
private void addUndefinedLiverTransporter()
{
var undefinedLiverTransporter = _individual.MoleculeByName <IndividualTransporter>(CoreConstants.Molecule.UndefinedLiverTransporter);
//Already added
if (undefinedLiverTransporter != null)
{
return;
}
undefinedLiverTransporter = _individualTransporterFactory.UndefinedLiverTransporterFor(_individual);
_individual.AddMolecule(undefinedLiverTransporter);
}
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.CreateFor(_individual).DowncastTo <IndividualEnzyme>().WithName("CYP");
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Plasma).Value = _relExpNormPls;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.BloodCells).Value = _relExpNormBloodCells;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.VascularEndothelium).Value = _relExpVascEndo;
_individual.AddMolecule(_enzyme);
_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.Parameter.CLspec).Value = 15;
_compound.AddProcess(_metabolizationProcess);
_simulationRunOptions = new SimulationRunOptions {
RaiseEvents = false
};
}
public IndividualTransporter AddUndefinedLiverTransporterTo(Individual individual)
{
var transporter = CreateMolecule(CoreConstants.Molecule.UndefinedLiverTransporter);
AddOntogenyParameterTo(transporter);
transporter.TransportType = TransportType.Efflux;
var liver = individual.Organism.Organ(CoreConstants.Organ.LIVER);
LiverZones.Each(zoneName =>
{
var zone = liver.Compartment(zoneName);
var intracellular = zone.Container(INTRACELLULAR);
addContainerExpression(intracellular, transporter, TransportDirectionId.ExcretionLiver,
RelExpParam(REL_EXP),
FractionParam(FRACTION_EXPRESSED_APICAL, CoreConstants.Rate.ONE_RATE),
InitialConcentrationParam(CoreConstants.Rate.INITIAL_CONCENTRATION_INTRACELLULAR_TRANSPORTER)
);
var relExpParameter = intracellular.EntityAt <IParameter>(transporter.Name, REL_EXP);
relExpParameter.Value = 1;
relExpParameter.DefaultValue = 1;
});
_individualPathWithRootExpander.AddRootToPathIn(individual, transporter.Name);
individual.AddMolecule(transporter);
return(transporter);
}
public IndividualEnzyme AddUndefinedLiverTo(Individual individual)
{
var undefinedLiver = CreateMolecule(CoreConstants.Molecule.UndefinedLiver);
AddOntogenyParameterTo(undefinedLiver);
undefinedLiver.Localization = Localization.Intracellular;
undefinedLiver.ReferenceConcentration.Visible = false;
undefinedLiver.HalfLifeLiver.Visible = false;
undefinedLiver.HalfLifeIntestine.Visible = false;
var liver = individual.Organism.Organ(CoreConstants.Organ.LIVER);
CoreConstants.Compartment.LiverZones.Each(zoneName =>
{
var zone = liver.Container(zoneName);
var intracellular = zone.Container(CoreConstants.Compartment.INTRACELLULAR);
AddContainerExpression(intracellular, undefinedLiver.Name,
RelExpParam(REL_EXP),
FractionParam(FRACTION_EXPRESSED_INTRACELLULAR, CoreConstants.Rate.ONE_RATE),
InitialConcentrationParam(CoreConstants.Rate.INITIAL_CONCENTRATION_INTRACELLULAR)
);
var relExpParameter = intracellular.EntityAt <IParameter>(undefinedLiver.Name, REL_EXP);
relExpParameter.Value = 1;
relExpParameter.DefaultValue = 1;
});
_individualPathWithRootExpander.AddRootToPathIn(individual, undefinedLiver.Name);
individual.AddMolecule(undefinedLiver);
return(undefinedLiver);
}
protected override void Context()
{
_protein = A.Fake <IndividualProtein>();
_context = A.Fake <IExecutionContext>();
_individual = new Individual();
_individual.AddMolecule(_protein);
sut = new RemoveMoleculeFromIndividualCommand(_protein, _individual, _context);
}
protected override void Context()
{
_interactionProcessRetriever = A.Fake <IInteractionProcessRetriever>();
_view = A.Fake <ISimulationCompoundInteractionSelectionView>();
sut = new SimulationCompoundInteractionSelectionPresenter(_view, _interactionProcessRetriever);
_interactionProperties = new InteractionProperties();
_allSimulationInteractionProcesses = new List <SimulationPartialProcess>();
_simulation = A.Fake <Simulation>();
var individual = new Individual().WithName("Enzyme");
_molecule1 = new IndividualEnzyme().WithName("CYP3A4");
_undefinedLiver = new IndividualEnzyme().WithName(CoreConstants.Molecule.UndefinedLiver);
individual.AddMolecule(_molecule1);
individual.AddMolecule(_undefinedLiver);
_interactionProcess1 = new InhibitionProcess().WithName("INTERACTION1");
_interactionProcess2 = new InhibitionProcess().WithName("INTERACTION2");
_interactionProcess3 = new InhibitionProcess().WithName("INTERACTION3");
var comp1 = new Compound();
comp1.AddProcess(_interactionProcess1);
var comp2 = new Compound();
comp2.AddProcess(_interactionProcess2);
comp2.AddProcess(_interactionProcess3);
_allSimulationInteractionProcesses.Add(new SimulationPartialProcess {
CompoundProcess = _interactionProcess1, IndividualMolecule = _molecule1
});
_allSimulationInteractionProcesses.Add(new SimulationPartialProcess {
CompoundProcess = _interactionProcess2, IndividualMolecule = _molecule1
});
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Individual).Returns(individual);
A.CallTo(() => _simulation.Compounds).Returns(new[] { comp1, comp2 });
A.CallTo(_interactionProcessRetriever).WithReturnType <IReadOnlyList <SimulationPartialProcess> >()
.Invokes(x => _useDefaultMap = x.GetArgument <bool>(2))
.Returns(_allSimulationInteractionProcesses);
A.CallTo(() => _view.BindTo(A <IEnumerable <SimulationInteractionProcessSelectionDTO> > ._))
.Invokes(x => _allSimulationInteractionProcessSelectionDTO = x.GetArgument <IEnumerable <SimulationInteractionProcessSelectionDTO> >(0));
}
public void Update(Individual sourceIndividual, Individual targetIndividual)
{
foreach (var molecule in sourceIndividual.AllMolecules())
{
var newMolecule = _cloner.Clone(molecule);
targetIndividual.AddMolecule(newMolecule);
//we have to reset the new ontogeny for the molecule
_ontogenyTask.SetOntogenyForMolecule(newMolecule, newMolecule.Ontogeny, targetIndividual);
}
}
protected IndividualEnzyme AddEnzymeTo(Individual individual, string enzymeName)
{
var enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
var enzyme = enzymeFactory.CreateFor(_individual).DowncastTo <IndividualEnzyme>().WithName(enzymeName);
enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Pericentral).Value = 1;
enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Periportal).Value = 1;
individual.AddMolecule(enzyme);
return(enzyme);
}
protected override void Context()
{
base.Context();
_allParameters.Clear();
_allParameters.Add(_para1);
_individual = new Individual().WithName("toto");
_individualMolecule = new IndividualEnzyme();
_para1.Name = CoreConstants.Parameters.REFERENCE_CONCENTRATION;
_individualMolecule.Add(_para1);
_individualMolecule.Name = "CYP3A4";
_individual.AddMolecule(_individualMolecule);
}
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);
}
protected override void Context()
{
_protein = new IndividualOtherProtein().WithName("CYP3A4");
_context = A.Fake <IExecutionContext>();
_organism = new Organism();
_liver = new Organ().WithName("liver").WithParentContainer(_organism);
_localMoleculeContainer = new Container().WithName(_protein.Name).WithParentContainer(_liver);
_individual = new Individual {
_organism
};
_individual.AddMolecule(_protein);
sut = new RemoveMoleculeFromIndividualCommand(_protein, _individual, _context);
}
public void Update(Individual sourceIndividual, Individual targetIndividual)
{
foreach (var molecule in sourceIndividual.AllMolecules())
{
var newMolecule = _cloner.Clone(molecule);
targetIndividual.AddMolecule(newMolecule);
//Make sure parameters that user defined parameters are reset to default to ensure proper scaling
resetMoleculeParametersToDefault(newMolecule);
//we have to reset the ontogeny for the molecule based on the target individual properties
_ontogenyTask.SetOntogenyForMolecule(newMolecule, newMolecule.Ontogeny, targetIndividual);
}
}