protected override void Context() { base.Context(); var displayUnitRetriever = IoC.Resolve <IDisplayUnitRetriever>(); var f1 = new ExplicitFormula("CL*conc").WithName("formula"); var r1 = new ReactionBuilder().WithName("Reaction").WithFormula(f1); r1.AddEduct(new ReactionPartnerBuilder("Drug", 1)); r1.AddEduct(new ReactionPartnerBuilder("Metab", 1)); r1.AddModifier("Cyp"); var concentrationDimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs(); var p1Formula = new ConstantFormula(2).WithDimension(concentrationDimension); var p11 = new Parameter().WithName("P1").WithFormula(p1Formula).WithParentContainer(r1); var f2 = new ExplicitFormula("CL*conc").WithName("formula"); var r2 = new ReactionBuilder().WithName("Reaction").WithFormula(f2); r2.AddEduct(new ReactionPartnerBuilder("Drug", 1)); r2.AddEduct(new ReactionPartnerBuilder("Metab", 1)); r2.AddModifier("Cyp"); var p12Forumla = new ConstantFormula(3).WithDimension(concentrationDimension); var p12 = new Parameter().WithName("P1").WithFormula(p12Forumla).WithParentContainer(r2); _object1 = r1; _object2 = r2; _preferredUnit = concentrationDimension.Units.ElementAt(0); A.CallTo(() => displayUnitRetriever.PreferredUnitFor(p1Formula, null)).Returns(_preferredUnit); A.CallTo(() => displayUnitRetriever.PreferredUnitFor(p12Forumla, null)).Returns(_preferredUnit); }
protected override void Context() { base.Context(); var reactionBuilder = new ReactionBuilder().WithName("R1"); _parameter = new Parameter().WithName("P1").WithMode(ParameterBuildMode.Local).WithParentContainer(reactionBuilder); }
protected override void Context() { _simulation = new ModelCoreSimulation(); var root = new Container(); root.Add(new EventGroup()); _simulation.Model = new Model(); _simulation.Model.Root = root; _simulation.BuildConfiguration = new BuildConfiguration(); var reactionBuildingBlock = new ReactionBuildingBlock(); var reactionAtoB = new ReactionBuilder(); var reactionBtoA = new ReactionBuilder(); var partnerA = new ReactionPartnerBuilder("A", 0); var partnerB = new ReactionPartnerBuilder("B", 0); //Making both reactions dependent on each other reactionAtoB.AddProduct(partnerA); reactionBtoA.AddProduct(partnerB); reactionAtoB.AddEduct(partnerB); reactionBtoA.AddEduct(partnerA); reactionBuildingBlock.Add(reactionAtoB); reactionBuildingBlock.Add(reactionBtoA); _simulation.BuildConfiguration.Reactions = reactionBuildingBlock; }
protected override void Context() { base.Context(); _project = new MoBiProject(); var molecule = new MoleculeBuilder().WithName(_moleculeName); var moleculeParameter = new Parameter().WithName(_moleculeParameterName); molecule.Add(moleculeParameter); var molecules = new MoleculeBuildingBlock() { molecule }; _project.AddBuildingBlock(molecules); var parameter = new Parameter().WithName(_parameterName); var root = new Container().WithName("Root"); root.Add(parameter); var spatialStructure = new MoBiSpatialStructure().WithTopContainer(root); _project.AddBuildingBlock(spatialStructure); var reactionBuilder = new ReactionBuilder().WithName(_reactionName); var reactions = new MoBiReactionBuildingBlock() { reactionBuilder }; _project.AddBuildingBlock(reactions); A.CallTo(() => _context.CurrentProject).Returns(_project); }
protected override void Context() { base.Context(); _reactionBuilder = new ReactionBuilder { Dimension = DomainHelperForSpecs.ConcentrationPerTimeDimension }; A.CallTo(() => _reactionDimensionRetriever.SelectedDimensionMode).Returns(ReactionDimensionMode.AmountBased); }
protected override void Context() { base.Context(); _reactionParameter = new Parameter().WithName("RP"); var reactionBuilder = new ReactionBuilder(); reactionBuilder.Add(_reactionParameter); }
protected ReactionBuilder createReaction() { var reaction = new ReactionBuilder(); reaction.AddEduct(new ReactionPartnerBuilder("educt", 1.0)); reaction.AddProduct(new ReactionPartnerBuilder("product", 1.0)); reaction.AddModifier("modifier"); return(reaction); }
protected override void Context() { _reactionBuildingBlock = new MoBiReactionBuildingBlock(); _moBiReactionDiagramManager = A.Fake <IMoBiReactionDiagramManager>(); _reactionBuildingBlock.DiagramManager = _moBiReactionDiagramManager; _reaction = new ReactionBuilder().WithName("R"); _reaction.AddModifier("old"); sut = new ChangeModifierCommand("new", "old", _reaction, _reactionBuildingBlock); }
protected IReactionBuilder CreateReactionForCompoundAndMetabolite(string[] products, params string[] educts) { var reaction = new ReactionBuilder(); educts.Each(educt => reaction.AddEduct(new ReactionPartnerBuilder(educt, 1))); products.Each(product => reaction.AddProduct(new ReactionPartnerBuilder(product, 1))); return(reaction); }
protected override void Context() { base.Context(); createReaction(); _sourceReaction = createReaction(); _targetReaction = new ReactionBuilder(); _sourceBuildingBlock.Add(_sourceReaction); _targetBuildingBlock.Add(_targetReaction); }
protected override void Context() { base.Context(); _sourceBuilder = new ReactionBuilder { Name = "builder" }; A.CallTo(() => _sourceBuildingBlock.DiagramModel.FindByName(_sourceBuilder.Name)).Returns(null); }
protected override void Context() { base.Context(); _formulaCache = new FormulaCache(); _protein = A.Fake <IMoleculeBuilder>().WithName("CYP3A4"); var reaction = new ReactionBuilder { Formula = new ExplicitFormula().WithName("ABC") }; reaction.Formula.AddObjectPath(new FormulaUsablePath(CoreConstants.KeyWords.Protein, "P1").WithAlias("P1")); reaction.Formula.AddObjectPath(new FormulaUsablePath(CoreConstants.KeyWords.Reaction, "R1").WithAlias("R1")); _template = A.Fake <IReactionBuilder>().WithName(CoreConstants.Reaction.TURNOVER); A.CallTo(() => _cloneManager.Clone(_template)).Returns(reaction); }
private IEnumerable <IReactionBuilder> getReactions() { var r1 = new ReactionBuilder(); r1.AddEduct(new ReactionPartnerBuilder("C", 2.0)); r1.AddProduct(new ReactionPartnerBuilder("D1", 1.0)); r1.Name = "name"; r1.WithKinetic(new ExplicitFormula("k1*C")); r1.Description = "description"; yield return(r1); yield return(A.Fake <IReactionBuilder>()); }
protected override void Context() { _quantity = _parameter; base.Context(); var reaction = new ReactionBuilder(); reaction.AddParameter(_parameter); var reactionBuildingBlock = new ReactionBuildingBlock { reaction }; _buildingBlockInfo.UntypedBuildingBlock = reactionBuildingBlock; }
protected override void Context() { _oldMoleculeName = "A"; _newMoleculeName = "B"; _reaction = new ReactionBuilder().WithId("R"); _reactionPartner = new ReactionPartnerBuilder(_oldMoleculeName, 3); _buildingBlock = A.Fake <IMoBiReactionBuildingBlock>().WithId("BB"); _context = A.Fake <IMoBiContext>(); A.CallTo(() => _context.Get <IReactionBuilder>(_reaction.Id)).Returns(_reaction); A.CallTo(() => _context.Get <IMoBiReactionBuildingBlock>(_buildingBlock.Id)).Returns(_buildingBlock); AddPartnerToReaction(); _diagramManager = A.Fake <IMoBiReactionDiagramManager>(); A.CallTo(() => _buildingBlock.DiagramManager).Returns(_diagramManager); sut = new EditReactionPartnerMoleculeNameCommand(_newMoleculeName, _reaction, _reactionPartner, _buildingBlock); }
protected override void Context() { base.Context(); createReaction(); _sourceReaction = createReaction(); _targetReaction = createReaction(); _sourceBuildingBlock.Add(_sourceReaction); _targetBuildingBlock = A.Fake <IMoBiReactionBuildingBlock>(); A.CallTo(_targetBuildingBlock).WithReturnType <IEnumerable <IReactionBuilder> >().Returns(new[] { _targetReaction }); var moleculeNodes = createMoleculeNodes(); A.CallTo(() => _targetBuildingBlock.AllMolecules).Returns(moleculeNodes.Select(x => x.Name)); }
protected override void Context() { base.Context(); _reaction1 = new ReactionBuilder().WithName("Reaction"); _parameter = new Parameter().WithName("ReferencFrom").WithParentContainer(_reaction1); _otherParameter = new Parameter().WithName("ToReference").WithParentContainer(_reaction1); _reaction2 = new ReactionBuilder().WithName("Reaction2"); _reaction3 = new ReactionBuilder().WithName("A Reaction"); _otherParameter2 = new Parameter().WithName("ToReference").WithParentContainer(_reaction2); _reactionBuilidingBlock = new ReactionBuildingBlock(); _reactionBuilidingBlock.Add(_reaction1); _reactionBuilidingBlock.Add(_reaction2); _reactionBuilidingBlock.Add(_reaction3); }
protected override void Context() { base.Context(); _reactionBuildingBlock = new ReactionBuildingBlock(); _firstNode = A.Fake <IBaseNode>(); A.CallTo(() => _firstNode.Id).Returns("Id1"); A.CallTo(() => _firstNode.Name).Returns("Name"); _secondBuilder = new ReactionBuilder { Name = "Name", Id = "Id2" }; _simulation.Reactions = _reactionBuildingBlock; _reactionBuildingBlock.Add(_secondBuilder); _diagramModel = A.Fake <IDiagramModel>(); A.CallTo(() => _simulation.ReactionDiagramModel).Returns(_diagramModel); A.CallTo(() => _diagramModel.FindByName(_secondBuilder.Name)).Returns(_firstNode); }
protected override void Context() { base.Context(); _targetBuildingBlock.Add(new ReactionBuilder { Name = "reactionName" }); _sourceBuilder = new ReactionBuilder { Name = "reactionName" }; _sourceBuildingBlock.Add(_sourceBuilder); _sourceNode = A.Fake <IBaseNode>(); _targetNode = A.Fake <IBaseNode>(); A.CallTo(() => _sourceBuildingBlock.DiagramModel.FindByName("reactionName")).Returns(_sourceNode); A.CallTo(() => _targetBuildingBlock.DiagramModel.FindByName("reactionName")).Returns(_targetNode); }
protected override void Context() { base.Context(); _project = new MoBiProject(); var molecule = new MoleculeBuilder().WithName(_moleculeName); var moleculeParameter = new Parameter().WithName(_moleculeParameterName); molecule.Add(moleculeParameter); var molecules = new MoleculeBuildingBlock() { molecule }; _project.AddBuildingBlock(molecules); var parameter = new Parameter().WithName(_parameterName); var root = new Container().WithName(_topContainerName); root.Add(parameter); var spatialStructure = new MoBiSpatialStructure().WithTopContainer(root); spatialStructure.GlobalMoleculeDependentProperties = new Container().WithName(Constants.MOLECULE_PROPERTIES); spatialStructure.NeighborhoodsContainer = new Container().WithName(Constants.NEIGHBORHOODS); _project.AddBuildingBlock(spatialStructure); var reactionBuilder = new ReactionBuilder().WithName(_reactionName); var reactions = new MoBiReactionBuildingBlock() { reactionBuilder }; _project.AddBuildingBlock(reactions); _project.AddSimulation(new MoBiSimulation().WithName(_simulationName)); var eventGroupBuilder = new EventGroupBuilder().WithName(_eventGroupName); var eventGroupBuildingBlock = new EventGroupBuildingBlock(); eventGroupBuildingBlock.Add(eventGroupBuilder); _project.AddBuildingBlock(eventGroupBuildingBlock); A.CallTo(() => _context.CurrentProject).Returns(_project); }
protected override void Context() { base.Context(); var f1 = new ExplicitFormula("CL*conc").WithName("formula"); var r1 = new ReactionBuilder().WithName("Reaction").WithFormula(f1); r1.AddEduct(new ReactionPartnerBuilder("Drug", 1)); r1.AddEduct(new ReactionPartnerBuilder("Metab", 1)); r1.AddModifier("Cyp"); var p11 = new Parameter().WithName("P1").WithFormula(new ConstantFormula(2)).WithParentContainer(r1); var f2 = new ExplicitFormula("CL*conc").WithName("formula"); var r2 = new ReactionBuilder().WithName("Reaction").WithFormula(f2); r2.AddEduct(new ReactionPartnerBuilder("Drug", 1)); r2.AddEduct(new ReactionPartnerBuilder("Metab2", 1)); r2.AddModifier("Cyp"); var p12 = new Parameter().WithName("P1").WithFormula(new ConstantFormula(2)).WithParentContainer(r2); _object1 = r1; _object2 = r2; }
protected override void Context() { base.Context(); _reactionBuildingBlock = new MoBiReactionBuildingBlock { DiagramModel = new DiagramModel(), DiagramManager = new MoBiReactionDiagramManager() }; _moBiReactionDiagramManager = _reactionBuildingBlock.DiagramManager.DowncastTo <IReactionDiagramManager <IMoBiReactionBuildingBlock> >(); _moBiReactionDiagramManager.InitializeWith(_reactionBuildingBlock, A.Fake <IDiagramOptions>()); _molecule = new MoleculeBuilder().WithId("moleculeId").WithName("moleculeName"); _reaction = new ReactionBuilder().WithId("reactionId"); _reaction.AddEduct(new ReactionPartnerBuilder(_molecule.Name, 1.0)); _reactionBuildingBlock.Add(_reaction); _moBiReactionDiagramManager.AddObjectBase(_reaction); _moBiReactionDiagramManager.AddMolecule(_reaction, "moleculeName"); _moleculeNode = _moBiReactionDiagramManager.GetMoleculeNodes("moleculeName").FirstOrDefault(); _reactionNode = _moBiReactionDiagramManager.PkModel.DiagramModel.GetAllChildren <ReactionNode>().FirstOrDefault(); _interactionTask = A.Fake <IInteractionTasksForChildren <IMoBiReactionBuildingBlock, IReactionBuilder> >(); _activeSubjectRetriever = A.Fake <IActiveSubjectRetriever>(); var reactionLink = new ReactionLink(); reactionLink.Initialize(ReactionLinkType.Educt, _reactionNode, _moleculeNode); sut.Edit(_reactionBuildingBlock); var removeReactionCommand = new RemoveCommandFor <IMoBiReactionBuildingBlock, IReactionBuilder>(_interactionTask, _moBiContext, _activeSubjectRetriever); A.CallTo(() => _moBiContext.Get <IReactionBuilder>(_reaction.Id)).Returns(_reaction); A.CallTo(() => _moBiContext.Resolve <RemoveCommandFor <IMoBiReactionBuildingBlock, IReactionBuilder> >()).Returns(removeReactionCommand); A.CallTo(() => _activeSubjectRetriever.Active <IBuildingBlock>()).Returns(_reactionBuildingBlock); A.CallTo(() => _interactionTask.Remove(_reaction, _reactionBuildingBlock, _reactionBuildingBlock, A <bool> ._)).Invokes(x => _reactionBuildingBlock.Remove(_reaction)); }
protected override void Context() { _reactionBuilder = new ReactionBuilder(); sut = new ReactionBuilderToObjectBaseSummaryDTOMapper(new StoichiometricStringCreator(new ReactionPartnerToReactionPartnerBuilderMapper()), new ObjectTypeResolver()); }
protected override void Context() { sut = new ReactionBuilder(); }
private MoBiCommand moveDiagramNodes(MoBiReactionBuildingBlock source, MoBiReactionBuildingBlock target) { IReactionBuilder sourceBuilder = new ReactionBuilder().WithName("sourceBuilder"); return(sut.MoveDiagramNodes(source, target, sourceBuilder, sourceBuilder.Name) as MoBiCommand); }
public override void Register() { Register(ReactionBuilder.For <IHomeStore>(SomeAction) .Observe(x => x.Value)); }