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(); }