protected override void Context()
{
base.Context();
_amountPerTimeDimension = A.Fake <IDimension>();
_transporterMoleculeContainer = new TransporterMoleculeContainer();
A.CallTo(() => _interactionTaskContext.DimensionByName(Constants.Dimension.AMOUNT_PER_TIME)).Returns(_amountPerTimeDimension);
}
private IContainer addActiveTransportToNeighborhood(INeighborhood neighborhood, ITransport transport,
TransporterMoleculeContainer transporterMolecule, string transportedMoleculeName, IBuildConfiguration buildConfiguration)
{
return(_moleculePropertiesContainerTask.NeighborhoodMoleculeTransportContainerFor(neighborhood, transportedMoleculeName, transporterMolecule,
transport.Name, buildConfiguration)
.WithChild(transport));
}
protected override void Context()
{
_quantity = A.Fake <IParameter>().WithName("P");
base.Context();
_parameter.Name = "P";
var moleculeBuilder1 = new MoleculeBuilder().WithName("Mol1");
var moleculeBuilder2 = new MoleculeBuilder().WithName("Mol2");
var transporterMolecule1 = new TransporterMoleculeContainer {
TransportName = "TRANSPORT", Name = "TRANSPORTER"
};
var molecule1 = new Container().WithName("Mol1");
molecule1.Add(transporterMolecule1);
var molecule2 = new Container().WithName("Mol2");
var transporterMolecule2 = new TransporterMoleculeContainer {
TransportName = "TRANSPORT", Name = "TRANSPORTER"
};
molecule2.Add(transporterMolecule2);
moleculeBuilder1.AddTransporterMoleculeContainer(transporterMolecule1);
moleculeBuilder2.AddTransporterMoleculeContainer(transporterMolecule2);
var moleculeBuildingBlock = new MoleculeBuildingBlock {
moleculeBuilder1, moleculeBuilder2
};
_buildingBlockInfo.UntypedBuildingBlock = moleculeBuildingBlock;
transporterMolecule1.AddParameter(_parameter);
_quantity.ParentContainer.Name = transporterMolecule1.TransportName;
_quantity.ParentContainer.ParentContainer.Name = moleculeBuilder1.Name;
}
protected override void Context()
{
_formulaCache = A.Fake <IFormulaCache>();
_repository = A.Fake <IRepository <IInteractionKineticUpdaterSpecification> >();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
A.CallTo(() => _objectBaseFactory.Create <ExplicitFormula>()).ReturnsLazily(x => new ExplicitFormula());
A.CallTo(() => _repository.All()).Returns(_allKineticUpdaterSpecifications);
sut = new InteractionKineticUpdater(_repository, _objectBaseFactory);
_reaction = new ReactionBuilder();
_transporterMoleculeContainer = new TransporterMoleculeContainer();
_simulation = A.Fake <Simulation>();
_interactionProperties = new InteractionProperties();
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _enzymeName, ProcessName = _processName
});
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
_kmFactor = new PKSimParameter().WithName(CoreConstants.Parameter.KM_INTERACTION_FACTOR).WithFormula(new ExplicitFormula("1"));
_vmaxFactor = new PKSimParameter().WithName(CoreConstants.Parameter.KCAT_INTERACTION_FACTOR).WithFormula(new ExplicitFormula("1"));
_reaction.Add(_kmFactor);
_reaction.Add(_vmaxFactor);
_transporterMoleculeContainer.Add(_kmFactor);
_transporterMoleculeContainer.Add(_vmaxFactor);
}
public ObjectBaseDTO MapFrom(TransporterMoleculeContainer transporterMoleculeContainer)
{
var dto = Map <ObjectBaseDTO>(transporterMoleculeContainer);
dto.Name = transporterMoleculeContainer.TransportName;
return(dto);
}
protected override void Context()
{
base.Context();
_parent = new MoleculeBuilder().WithName("Drug");
_interactionContainer = new InteractionContainer().WithParentContainer(_parent);
_parameter = new Parameter().WithName("P1").WithParentContainer(_parent);
_transporterMolecule = new TransporterMoleculeContainer().WithName("PGP").WithParentContainer(_parent);
}
public TransporterMoleculeContainerDTO MapFrom(TransporterMoleculeContainer transporterMoleculeContainer)
{
var dto = Map <TransporterMoleculeContainerDTO>(transporterMoleculeContainer);
dto.TransportName = transporterMoleculeContainer.TransportName;
dto.Realizations = transporterMoleculeContainer.ActiveTransportRealizations.MapAllUsing(_activeTransportToDTOActiveTransportBuilderMapper);
dto.Parameters = transporterMoleculeContainer.Parameters.MapAllUsing(_parameterBuilderToDTOParameterBuilderMapper).Cast <ParameterDTO>();
return(dto);
}
protected override void Context()
{
base.Context();
_clSpecFactor = new Parameter().WithFormula(new ExplicitFormula());
_transporterMoleculeContainer = new TransporterMoleculeContainer();
_interactionProperties.ClearInteractions();
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _competitiveInhibition2.Name, CompoundName = _compound2.Name
});
}
protected override void Context()
{
base.Context();
_activeTransportBuilderContainer = new TransporterMoleculeContainer();
_buildingBlock = A.Fake <IMoleculeBuildingBlock>();
_dto = new TransporterMoleculeContainerDTO();
A.CallTo(() => _transporterMoleculeContainerMapper.MapFrom(_activeTransportBuilderContainer)).Returns(_dto);
sut.BuildingBlock = _buildingBlock;
sut.Edit(_activeTransportBuilderContainer);
}
protected override void Context()
{
base.Context();
_transporterMoleculeContainer = A.Fake <TransporterMoleculeContainer>();
_transporterMoleculeContainer.Name = "Cyp";
_parameter = A.Fake <IParameter>();
_transporter = A.Fake <ITransportBuilder>();
A.CallTo(() => _transporterMoleculeContainer.ActiveTransportRealizations).Returns(new [] { _transporter });
A.CallTo(() => _transporterMoleculeContainer.Parameters).Returns(new[] { _parameter });
}
public void Visit(TransporterMoleculeContainer transporterMoleculeContainer)
{
checkObjectBase(transporterMoleculeContainer);
if (!string.Equals(_oldName, transporterMoleculeContainer.TransportName))
{
return;
}
_changes.Add(transporterMoleculeContainer, _buildingBlock,
new EditObjectBasePropertyInBuildingBlockCommand(_tranportNamePropertyName, _newName, _oldName, transporterMoleculeContainer, _buildingBlock),
AppConstants.Commands.EditDescription(_objectTypeResolver.TypeFor <TransporterMoleculeContainer>(), _tranportNamePropertyName, _oldName, _newName, transporterMoleculeContainer.Name));
}
private void addActiveTransportToModel(IModel model, ITransportBuilder activeTransportBuilder, IEnumerable <INeighborhood> allNeighborhoods,
IMoleculeBuilder molecule, TransporterMoleculeContainer transporterMolecule, IBuildConfiguration buildConfiguration)
{
var neighborhoods = getNeighborhoodsForActiveTransport(activeTransportBuilder, allNeighborhoods, molecule.Name, transporterMolecule.Name);
foreach (var neighborhood in neighborhoods)
{
var activeTransport = mapFrom(activeTransportBuilder, neighborhood, molecule.Name, buildConfiguration);
var activeTransportInMolecule =
addActiveTransportToNeighborhood(neighborhood, activeTransport, transporterMolecule, molecule.Name, buildConfiguration);
buildConfiguration.AddBuilderReference(activeTransportInMolecule, activeTransportBuilder);
_keywordReplacerTask.ReplaceIn(activeTransport, model.Root, molecule.Name, neighborhood, transporterMolecule.TransportName,
transporterMolecule.Name);
}
}
protected override void Context()
{
base.Context();
_moleculeBuilder = A.Fake <IMoleculeBuilder>();
_startFormula = A.Fake <IFormula>();
_moleculeBuilder.DefaultStartFormula = _startFormula;
_moleculeBuilder.Description = "Description";
_moleculeBuilder.Icon = "Icon";
_moleculeBuilder.Id = "ID";
_moleculeBuilder.IsFloating = true;
_moleculeBuilder.QuantityType = QuantityType.Drug;
_activeTransport = A.Fake <ITransportBuilder>();
_transporterMoleculeContainer = A.Fake <TransporterMoleculeContainer>();
A.CallTo(() => _moleculeBuilder.TransporterMoleculeContainerCollection).Returns(new[] { _transporterMoleculeContainer });
A.CallTo(() => _transporterMoleculeContainer.ActiveTransportRealizations).Returns(new[] { _activeTransport });
_parameter = A.Fake <IParameter>();
A.CallTo(() => _moleculeBuilder.Parameters).Returns(new[] { _parameter });
_calculationMethod = A.Fake <UsedCalculationMethod>();
A.CallTo(() => _moleculeBuilder.UsedCalculationMethods).Returns(new[] { _calculationMethod });
_interactionContainer = A.Fake <InteractionContainer>();
A.CallTo(() => _moleculeBuilder.InteractionContainerCollection).Returns(new[] { _interactionContainer });
}
public void Visit(TransporterMoleculeContainer transporterMoleculeContainer)
{
addNamesToHash(_nameHashForVisitor, For(transporterMoleculeContainer));
}
public void UpdateTransport(TransporterMoleculeContainer transporterMoleculeContainer, string compoundName, string transportedMolecule, Simulation simulation, IFormulaCache formulaCache)
{
updateProcess(transporterMoleculeContainer, compoundName, transportedMolecule, simulation, formulaCache);
}
protected IMenuBarItem CreateRenameItemFor(TransporterMoleculeContainer objectToEdit)
{
return(CreateMenuButton.WithCaption(AppConstants.MenuNames.Rename)
.WithCommandFor <RenameObjectCommand <TransporterMoleculeContainer>, TransporterMoleculeContainer>(objectToEdit)
.WithIcon(ApplicationIcons.Rename));
}
protected virtual IMenuBarItem CreateRemoveItemFor(TransporterMoleculeContainer objectToEdit)
{
return(CreateMenuButton.WithCaption(AppConstants.MenuNames.Delete)
.WithRemoveCommand(objectToEdit.ParentContainer.DowncastTo <IMoleculeBuilder>(), objectToEdit)
.WithIcon(ApplicationIcons.Delete));
}
public IEnumerable <string> For(TransporterMoleculeContainer transporterMoleculeContainer)
{
return(allLocalParametersFromMoleculesInProject());
}
protected virtual IMenuBarItem CreateAddExistingFromTemplateTransportFor(TransporterMoleculeContainer selectedObject)
{
return(CreateMenuButton.WithCaption(AppConstants.MenuNames.AddExistingFromTemplate("Transport"))
.WithCommandFor <AddExistingFromTemplateCommandFor <TransporterMoleculeContainer, ITransportBuilder>, TransporterMoleculeContainer>(selectedObject)
.WithIcon(ApplicationIcons.LoadFromTemplate));
}
public IContainer NeighborhoodMoleculeTransportContainerFor(INeighborhood neighborhood, string transportedMoleculeName, TransporterMoleculeContainer transporterMolecule, string transportName, IBuildConfiguration buildConfiguration)
{
var moleculeContainer = NeighborhoodMoleculeContainerFor(neighborhood, transportedMoleculeName);
var transportContainer = moleculeContainer.EntityAt <IContainer>(transporterMolecule.TransportName);
if (transportContainer != null)
{
return(transportContainer);
}
return(_containerTask.CreateOrRetrieveSubContainerByName(moleculeContainer, transporterMolecule.TransportName)
.WithChildren(allLocalParametersFrom(transporterMolecule, buildConfiguration)));
}
