protected override void Context()
{
base.Context();
var transportbuilder = new TransportBuilder().WithName("Trans");
transportbuilder.AddMoleculeNameToExclude(_oldName);
var transportbuilder2 = new TransportBuilder().WithName("Trans2");
transportbuilder2.AddMoleculeName(_oldName);
_test = new PassiveTransportBuildingBlock().WithName("Test");
_test.Add(transportbuilder);
_test.Add(transportbuilder2);
}
protected override void Context()
{
base.Context();
_passiveTransportBuildingBlock = new PassiveTransportBuildingBlock();
var pt1 = new TransportBuilder().WithName("T1");
new Parameter().WithName("LP").WithMode(ParameterBuildMode.Local).WithParentContainer(pt1);
new Parameter().WithName("PP").WithMode(ParameterBuildMode.Property).WithParentContainer(pt1);
new Parameter().WithName("GP").WithMode(ParameterBuildMode.Global).WithParentContainer(pt1);
_passiveTransportBuildingBlock.Add(pt1);
var pt2 = new TransportBuilder().WithName("T2");
new Parameter().WithName("LP").WithMode(ParameterBuildMode.Local).WithParentContainer(pt2);
new Parameter().WithName("PP").WithMode(ParameterBuildMode.Property).WithParentContainer(pt2);
new Parameter().WithName("GP").WithMode(ParameterBuildMode.Global).WithParentContainer(pt2);
_passiveTransportBuildingBlock.Add(pt2);
}
protected override void Context()
{
base.Context();
_project = A.Fake <IMoBiProject>();
_kinetic = new ExplicitFormula("GallbladderEmptyingRate");
_transportBuilder = new TransportBuilder().WithName("GallbladderEmptying").WithKinetic(_kinetic);
_buildingBlock = new PassiveTransportBuildingBlock();
_buildingBlock.Add(_transportBuilder);
}
protected override void Context()
{
_buildConfiguration = new MoBiBuildConfiguration();
_moleculeBuidingBlock = new MoleculeBuildingBlock().WithName("M");
_buildConfiguration.Molecules = _moleculeBuidingBlock;
_reactionBuildingBlock = new MoBiReactionBuildingBlock().WithName("R");
_reactionBuildingBlock.Add(new ReactionBuilder().WithName("R1"));
_buildConfiguration.Reactions = _reactionBuildingBlock;
_passiveTransportBuildingBlock = new PassiveTransportBuildingBlock().WithName("PT");
_passiveTransportBuildingBlock.Add(new TransportBuilder().WithName("PT2"));
_passiveTransportBuildingBlock.Add(new TransportBuilder().WithName("PT1"));
_buildConfiguration.PassiveTransports = _passiveTransportBuildingBlock;
_eventGroupBuildingBlock = new EventGroupBuildingBlock().WithName("EG");
_buildConfiguration.EventGroups = _eventGroupBuildingBlock;
_msvBuildingBlock = new MoleculeStartValuesBuildingBlock().WithName("MSV");
_buildConfiguration.MoleculeStartValues = _msvBuildingBlock;
_psvBuildingBlock = new ParameterStartValuesBuildingBlock().WithName("PSV");
_buildConfiguration.ParameterStartValues = _psvBuildingBlock;
_spatialStructure = new MoBiSpatialStructure().WithName("SPST");
_buildConfiguration.SpatialStructure = _spatialStructure;
_observerBuildingBlock = new ObserverBuildingBlock().WithName("O");
_buildConfiguration.Observers = _observerBuildingBlock;
_objectPathFactory = new ObjectPathFactory(new AliasCreator());
_entityPathResolver = new EntityPathResolver(_objectPathFactory);
sut = new AffectedBuildingBlockRetriever(_entityPathResolver);
//common setup
_simulation = new MoBiSimulation {
BuildConfiguration = _buildConfiguration
};
}
private void addTransportProcess(IMoleculeBuilder drug, IProcessMapping compoundProcessMapping, CompoundProperties compoundProperties)
{
var compound = compoundProperties.Compound;
var process = compound.ProcessByName(compoundProcessMapping.ProcessName);
if (isRenalClearance(compoundProcessMapping))
{
var renalPassiveProcess = _processBuilderMapper.PassiveTransportProcessFrom(process, drug.Name, _passiveTransports.FormulaCache);
_passiveTransports.Add(renalPassiveProcess);
_parameterIdUpdater.UpdateBuildingBlockId(renalPassiveProcess.Parameters, compound);
return;
}
var transporter = _individual.MoleculeByName <IndividualTransporter>(compoundProcessMapping.MoleculeName);
var transporterMoleculeContainer = _processBuilderMapper.ActiveTransportFrom(process, transporter, _moleculeBuildingBlock.FormulaCache);
_interactionKineticUpdater.UpdateTransport(transporterMoleculeContainer, compoundProcessMapping.MoleculeName, compound.Name, _simulation, _moleculeBuildingBlock.FormulaCache);
_parameterIdUpdater.UpdateBuildingBlockId(transporterMoleculeContainer.Parameters, compound);
drug.AddTransporterMoleculeContainer(transporterMoleculeContainer);
}
/// <summary>
/// Imports a SBML Reaction by creating a passive Transport.
/// </summary>
private void CreatePassiveTransport(Reaction sbmlReaction, Model model)
{
var reactant = sbmlReaction.getReactant(0).getSpecies();
var product = sbmlReaction.getProduct(0).getSpecies();
var reactantSpecies = GetSpeciesById(reactant, model);
var productSpecies = GetSpeciesById(product, model);
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != reactant)))
{
return;
}
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != product)))
{
return;
}
var molInfoReactant = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Contains(reactant));
var molInfoProduct = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Contains(product));
if (molInfoProduct == null)
{
return;
}
if (molInfoReactant == null)
{
return;
}
//must be the same Molecule
if (molInfoReactant.GetMoleculeBuilder() != molInfoProduct.GetMoleculeBuilder())
{
CreateErrorMessage();
}
var passiveTransport = ObjectBaseFactory.Create <ITransportBuilder>().WithName(sbmlReaction.getId());
passiveTransport.ForAll = false;
if (molInfoReactant.GetMoleculeBuilderName() == null)
{
return;
}
passiveTransport.MoleculeList.AddMoleculeName(molInfoReactant.GetMoleculeBuilderName());
var reactantCompartment = GetContainerFromCompartment_(molInfoReactant.GetCompartment(reactantSpecies));
var productCompartment = GetContainerFromCompartment_(molInfoProduct.GetCompartment(productSpecies));
if (reactantCompartment != null && productCompartment != null)
{
var reactantMatchTag = new MatchTagCondition(reactantCompartment.Name);
var productMatchTag = new MatchTagCondition(productCompartment.Name);
passiveTransport.SourceCriteria.Add(reactantMatchTag);
passiveTransport.TargetCriteria.Add(productMatchTag);
}
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(passiveTransport.AddParameter);
}
CreateKinetic(sbmlReaction, passiveTransport);
AddNeighbourhood(reactantCompartment, productCompartment, model);
_passiveTransportBuildingBlock.Add(passiveTransport);
}