protected override void Context()
{
base.Context();
_moleculeBuildingBlock = new MoleculeBuildingBlock();
_moleculeBuildingBlock.Add(new MoleculeBuilder().WithName("Drug"));
_moleculeBuildingBlock.Add(new MoleculeBuilder().WithName("Transporter"));
}
public override void GlobalContext()
{
base.GlobalContext();
_simulation = DomainFactoryForSpecs.CreateDefaultSimulation();
_moleculeBuildingBlock = new MoleculeBuildingBlock();
var compoundProperties = _simulation.CompoundPropertiesList.First();
_compoundName = compoundProperties.Compound.Name;
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = _compoundName, QuantityType = QuantityType.Drug
});
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = "Enzyme", QuantityType = QuantityType.Enzyme
});
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = "Metabolite", QuantityType = QuantityType.Metabolite
});
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = "Protein", QuantityType = QuantityType.OtherProtein
});
var specificBindingSelection = new ProcessSelection {
CompoundName = _compoundName, MoleculeName = "Protein", ProcessName = "Specific Binding"
};
var metabolizationSelection = new EnzymaticProcessSelection {
CompoundName = _compoundName, MoleculeName = "Protein", ProcessName = "Metabolism"
};
_complexProductName = specificBindingSelection.ProductName(CoreConstants.Molecule.Complex);
_metaboliteProductName = specificBindingSelection.ProductName(CoreConstants.Molecule.Metabolite);
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = _complexProductName, QuantityType = QuantityType.Complex
});
compoundProperties.Processes.SpecificBindingSelection.AddPartialProcessSelection(specificBindingSelection);
compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(metabolizationSelection);
}
protected override void Context()
{
base.Context();
_moleculeBuildingBlock = new MoleculeBuildingBlock {
Id = "1"
};
_moleculeBuildingBlock.Add(A.Fake <IMoleculeBuilder>().WithId("2"));
_moleculeBuildingBlock.Add(A.Fake <IMoleculeBuilder>().WithId("3"));
}
/// <summary>
/// Creates one dummy Species for each Compartment.
/// </summary>
private void CreateDummySpecies()
{
foreach (var child in GetMainTopContainer().GetAllChildren <IContainer>())
{
if (child.Name == Constants.MOLECULE_PROPERTIES)
{
continue;
}
var mbuilder = _moleculeBuilderFactory.Create(MoleculeBuildingBlock.FormulaCache)
.WithName(SBMLConstants.SBML_DUMMYSPECIES + child.Name)
.WithDescription(SBMLConstants.SBML_DUMMYSPECIES + child.Name);
MoleculeBuildingBlock.Add(mbuilder);
_sbmlInformation.DummyNameContainerDictionary[mbuilder.Name] = child.Name;
}
}
protected override void Context()
{
base.Context();
_moleculeBuildingBlock = new MoleculeBuildingBlock();
sut.Edit(_moleculeBuildingBlock);
_moleculeBuilder = new MoleculeBuilder();
_moleculeBuildingBlock.Add(_moleculeBuilder);
}
protected override void Context()
{
sut = new FormulaUsageChecker();
_formula = new ExplicitFormula("1").WithName("Test Formula");
_buildingBlock = new MoleculeBuildingBlock();
_moleculeBuilder = new MoleculeBuilder().WithName("Container");
_moleculeBuilder.DefaultStartFormula = A.Fake <IFormula>();
_buildingBlock.Add(_moleculeBuilder);
}
protected override void Context()
{
_moleculeBuildingBlock = new MoleculeBuildingBlock();
_molecule1 = new MoleculeBuilder {
Name = "M1", IsFloating = true
};
_molecule2 = new MoleculeBuilder {
Name = "M2", IsFloating = true
};
_molecule3 = new MoleculeBuilder {
Name = "M3", IsFloating = false
};
_moleculeBuildingBlock.Add(_molecule1);
_moleculeBuildingBlock.Add(_molecule2);
_moleculeBuildingBlock.Add(_molecule3);
_validParameter = new Parameter().WithFormula(new ConstantFormula(5)).WithName("_validParameter");
_invalidParameter = new Parameter().WithFormula(new ConstantFormula(double.NaN)).WithName("_invalidParameter");
_invalidParameterWithFormula = new Parameter().WithFormula(new ExplicitFormula("0/0")).WithName("_invalidParameterWithFormula");
_molecule3.AddParameter(_invalidParameter);
sut = new MoleculeBuildingBlockValidator();
}
protected override void Context()
{
base.Context();
_molecules = new MoleculeBuildingBlock();
_molecules.Add(createMoleculeBuilder("Drug"));
_molecules.Add(createMoleculeBuilder("Other"));
_spatialStrcuture = new SpatialStructure();
_spatialStrcuture.NeighborhoodsContainer = new Container().WithName(Constants.NEIGHBORHOODS);
_spatialStrcuture.GlobalMoleculeDependentProperties = new Container();
_globalParameter = new Parameter().WithName("GlobalMoleculeParameter").WithFormula(new ConstantFormula(2));
_spatialStrcuture.GlobalMoleculeDependentProperties.Add(_globalParameter);
var topcontainer = new Container().WithName("Organism");
var organ = new Container().WithName("Organ").WithParentContainer(topcontainer);
var mp = new Container().WithName(Constants.MOLECULE_PROPERTIES).WithParentContainer(organ);
new Parameter().WithName("Local").WithFormula(new ConstantFormula(3)).WithParentContainer(mp);
_spatialStrcuture.AddTopContainer(topcontainer);
var neighborhood = new NeighborhoodBuilder().WithName("A2B");
var nmp = new Container().WithName(Constants.MOLECULE_PROPERTIES).WithParentContainer(neighborhood);
new Parameter().WithName("Hallo").WithFormula(new ConstantFormula(4)).WithParentContainer(nmp);
_spatialStrcuture.AddNeighborhood(neighborhood);
}
private void addMoleculeToBuildingBlock(IMoleculeBuilder moleculeBuilder, CompoundProperties compoundProperties)
{
if (_allMoleculeNames.Contains(moleculeBuilder.Name))
{
throw new TwoMoleculesWithSameNameException(moleculeBuilder.Name);
}
_allMoleculeNames.Add(moleculeBuilder.Name);
//set the used calculation method according to current settings
if (compoundProperties != null)
{
_moleculeCalculationRetriever.AllMoleculeCalculationMethodsUsedBy(compoundProperties).Each(moleculeBuilder.AddUsedCalculationMethod);
}
_moleculeBuildingBlock.Add(moleculeBuilder);
}
public override void GlobalContext()
{
base.GlobalContext();
var compound = DomainFactoryForSpecs.CreateStandardCompound();
var individual = DomainFactoryForSpecs.CreateStandardIndividual();
var protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_simulation = _simulation = DomainFactoryForSpecs.CreateSimulationWith(individual, compound, protocol, CoreConstants.Model.TwoPores) as IndividualSimulation;
_moleculeBuildingBlock = new MoleculeBuildingBlock();
var compoundProperties = _simulation.CompoundPropertiesList.First();
_compoundName = compoundProperties.Compound.Name;
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = _compoundName, QuantityType = QuantityType.Drug
});
_observerName = CoreConstants.Observer.ObserverNameFrom("Whole Organ incl. FcRn_Complex", _compoundName);
}
protected override void Context()
{
base.Context();
_eventBuildingBlock = new EventGroupBuildingBlock().WithName("Events");
_applicationBuilder = new ApplicationBuilder().WithName("Tada");
_applicationBuilder.MoleculeName = "B";
_eventBuildingBlock.Add(_applicationBuilder);
_molceuleBuidingBlock = new MoleculeBuildingBlock().WithName("Molecules");
_molceuleBuidingBlock.Add(new MoleculeBuilder().WithName("A"));
_buildConfiguration = new BuildConfiguration();
_buildConfiguration.Molecules = _molceuleBuidingBlock;
_buildConfiguration.MoleculeStartValues = new MoleculeStartValuesBuildingBlock();
_buildConfiguration.Observers = new ObserverBuildingBlock();
_buildConfiguration.ParameterStartValues = new ParameterStartValuesBuildingBlock();
_buildConfiguration.PassiveTransports = new PassiveTransportBuildingBlock();
_buildConfiguration.Reactions = new ReactionBuildingBlock();
_buildConfiguration.SpatialStructure = new SpatialStructure();
_buildConfiguration.EventGroups = _eventBuildingBlock;
}
public override void GlobalContext()
{
base.GlobalContext();
var compound = DomainFactoryForSpecs.CreateStandardCompound();
var individual = DomainFactoryForSpecs.CreateStandardIndividual();
var protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_simulation = DomainFactoryForSpecs.CreateSimulationWith(individual, compound, protocol, CoreConstants.Model.TwoPores).DowncastTo <IndividualSimulation>();
_moleculeBuildingBlock = new MoleculeBuildingBlock();
var compoundProperties = _simulation.CompoundPropertiesList.First();
_compoundName = compoundProperties.Compound.Name;
_moleculeBuildingBlock.Add(new MoleculeBuilder {
Name = _compoundName, QuantityType = QuantityType.Drug
});
_observerName = CoreConstants.Observer.ObserverNameFrom(CoreConstantsForSpecs.Observer.WHOLE_ORGAN_INCLUDING_FCRN_COMPLEX, _compoundName);
}
protected override void Context()
{
_moleculeBuildingBlock = new MoleculeBuildingBlock {
Id = "Id"
};
_builder = new MoleculeBuilder {
Name = "name"
};
_moleculeBuildingBlock.Add(_builder);
_spatialStructure = new SpatialStructure();
var firstContainer = new Container {
Name = _firstPathEntry
};
firstContainer.Add(new Container {
Name = "Path", Mode = _containerMode
});
_spatialStructure.Add(firstContainer);
_moleculeStartValue = new MoleculeStartValue {
Name = _moleculeName, ContainerPath = new ObjectPath("The", "Path")
};
sut = new MoleculeResolver();
}