public SimulationProperties()
{
ModelProperties = new ModelProperties();
_compoundPropertiesList = new List <CompoundProperties>();
EventProperties = new EventProperties();
InteractionProperties = new InteractionProperties();
AllowAging = false;
Origin = Origins.PKSim;
}
/// <summary>
/// Returns a clone of the current simulation properties
/// </summary>
public virtual SimulationProperties Clone(ICloneManager cloneManager)
{
var clone = new SimulationProperties
{
ModelProperties = ModelProperties.Clone(cloneManager),
EventProperties = EventProperties.Clone(cloneManager),
InteractionProperties = InteractionProperties.Clone(cloneManager),
AllowAging = AllowAging,
Origin = Origin
};
_compoundPropertiesList.Each(cp => clone.AddCompoundProperties(cp.Clone(cloneManager)));
return(clone);
}
public Simulation CreateFrom(ISimulationSubject simulationSubject, IReadOnlyList <Compound> compounds, ModelProperties modelProperties, Simulation originalSimulation = null)
{
var simulation = createSimulation(simulationSubject.GetType());
//update the used building block in the simulation
originalSimulation?.UsedBuildingBlocks.Each(simulation.AddUsedBuildingBlock);
_simulationBuildingBlockUpdater.UpdateUsedBuildingBlockInSimulationFromTemplate(simulation, simulationSubject, PKSimBuildingBlockType.SimulationSubject);
_simulationBuildingBlockUpdater.UpdateMultipleUsedBuildingBlockInSimulationFromTemplate(simulation, compounds, PKSimBuildingBlockType.Compound);
//set basic properties
if (originalSimulation != null)
{
simulation.UpdateFromOriginalSimulation(originalSimulation);
simulation.Properties = originalSimulation.Properties;
}
//last but not least, update model properties to match new definition (this should be done last as UpdateFromOriginalSimulation resets the model properties)
simulation.ModelProperties = modelProperties;
updateCompoundProperties(simulation);
return(simulation);
}
private void addModelStructureTo(IContainer container, OriginData originData, ModelProperties modelProperties, IFormulaCache formulaCache)
{
_parameterContainerTask.AddModelParametersTo(container, originData, modelProperties, formulaCache);
foreach (var subContainer in _modelContainerQuery.SubContainersFor(originData.SpeciesPopulation, modelProperties.ModelConfiguration, container))
{
container.Add(subContainer);
addModelStructureTo(subContainer, originData, modelProperties, formulaCache);
}
}
private void addNeighborhood(INeighborhoodBuilder neighborhood, ISpatialStructure spatialStructure, OriginData originData, ModelProperties modelProperties, IFormulaCache formulaCache)
{
spatialStructure.AddNeighborhood(neighborhood);
_parameterContainerTask.AddModelParametersTo(neighborhood, originData, modelProperties, formulaCache);
_parameterContainerTask.AddModelParametersTo(neighborhood.MoleculeProperties, originData, modelProperties, formulaCache);
}
private void addNeighborhoods(ISpatialStructure spatialStructure, Organism organism, Individual individual, ModelProperties modelProperties, IFormulaCache formulaCache)
{
var neighborhoodList = _modelNeighborhoodQuery.NeighborhoodsFor(individual.Neighborhoods, modelProperties).ToList();
foreach (var neighborhood in neighborhoodList)
{
addNeighborhood(neighborhood, spatialStructure, individual.OriginData, modelProperties, formulaCache);
}
_neighborhoodFinalizer.SetNeighborsIn(organism, neighborhoodList);
}