public Simulation CreateSimulation(SimulationConstruction simulationConstruction, Action <Simulation> preModelCreationAction = null)
{
var sim = CreateModelLessSimulationWith(simulationConstruction);
preModelCreationAction?.Invoke(sim);
AddModelToSimulation(sim);
return(sim);
}
public Simulation CreateModelLessSimulationWith(SimulationConstruction simulationConstruction)
{
var sim = _simulationFactory.CreateFrom(simulationConstruction.SimulationSubject, simulationConstruction.TemplateCompounds, simulationConstruction.ModelProperties);
sim.Name = simulationConstruction.SimulationName;
for (int index = 0; index < simulationConstruction.TemplateCompounds.Count; index++)
{
var compoundProperties = sim.CompoundPropertiesList[index];
var compound = compoundProperties.Compound;
//for now: only simple protocol
var simpleProtocol = simulationConstruction.TemplateProtocols[index] as SimpleProtocol;
if (simpleProtocol != null && simpleProtocol.ApplicationType.NeedsFormulation && simulationConstruction.TemplateFormulation != null)
{
simpleProtocol.FormulationKey = simulationConstruction.TemplateFormulation.Name;
compoundProperties.ProtocolProperties.AddFormulationMapping(new FormulationMapping {
FormulationKey = simulationConstruction.TemplateFormulation.Name, TemplateFormulationId = simulationConstruction.TemplateFormulation.Id
});
}
var processes = compoundProperties.Processes;
//add all systemic processes
addSystemicProcesses(compound, processes.MetabolizationSelection, SystemicProcessTypes.Hepatic);
addSystemicProcesses(compound, processes.TransportAndExcretionSelection, SystemicProcessTypes.GFR);
addSystemicProcesses(compound, processes.TransportAndExcretionSelection, SystemicProcessTypes.Renal);
addSystemicProcesses(compound, processes.TransportAndExcretionSelection, SystemicProcessTypes.Biliary);
//add all partial processes
var individual = simulationConstruction.SimulationSubject as Individual ?? simulationConstruction.SimulationSubject.DowncastTo <Population>().FirstIndividual;
addPartialProcesses <EnzymaticProcess, IndividualEnzyme, EnzymaticProcessSelection>(compound, individual, processes.MetabolizationSelection);
addPartialProcesses <TransportPartialProcess, IndividualTransporter, ProcessSelection>(compound, individual, processes.TransportAndExcretionSelection);
addPartialProcesses <SpecificBindingPartialProcess, IndividualMolecule, ProcessSelection>(compound, individual, processes.SpecificBindingSelection);
_buildingBlockUpdater.UpdateMultipleUsedBuildingBlockInSimulationFromTemplate(sim, simulationConstruction.TemplateProtocols.Where(p => p != null), PKSimBuildingBlockType.Protocol);
var templateProtocol = simulationConstruction.TemplateProtocols[index];
if (templateProtocol != null)
{
compoundProperties.ProtocolProperties.Protocol = sim.AllBuildingBlocks <Protocol>().FindByName(templateProtocol.Name);
}
if (simulationConstruction.TemplateFormulation != null)
{
_buildingBlockUpdater.UpdateMultipleUsedBuildingBlockInSimulationFromTemplate(sim, new[] { simulationConstruction.TemplateFormulation }, PKSimBuildingBlockType.Formulation);
}
}
simulationConstruction.Interactions.Each(sim.InteractionProperties.AddInteraction);
sim.AllowAging = simulationConstruction.AllowAging;
return(sim);
}
public static Simulation CreateModelLessSimulationWith(ISimulationSubject simulationSubject, IReadOnlyList <Compound> compounds, IReadOnlyList <Protocol> protocols
, ModelProperties modelProperties, bool allowAging = false)
{
var simConstructor = IoC.Resolve <ISimulationConstructor>();
var simulationConstruction = new SimulationConstruction
{
SimulationSubject = simulationSubject,
TemplateCompounds = compounds,
TemplateProtocols = protocols,
ModelProperties = modelProperties,
SimulationName = "simulation",
AllowAging = allowAging,
};
return(simConstructor.CreateModelLessSimulationWith(simulationConstruction));
}