private IMoBiSimulation createSimulation(IModel model)
{
//update the building block configuration to now use clones
var simulationBuildConfiguration = _buildConfigurationFactory.CreateFromTemplateClones(_buildConfiguration);
var simulation = _simulationFactory.CreateFrom(simulationBuildConfiguration, model).WithName(_simulationDTO.Name);
simulation.HasChanged = true;
return(simulation);
}
private void createSimulation(Simulation originalSimulation)
{
//nothing changed
if (SimulationCreated)
{
return;
}
Simulation = _simulationFactory.CreateFrom(selectedSubject, selectedCompounds, modelSelectionPresenter.ModelProperties, originalSimulation);
Simulation.AllowAging = subjectConfigurationPresenter.AllowAging;
SimulationCreated = true;
}
public Model.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 Model.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);
}
private Task <IndividualSimulation> createNewSimulationBasedOn(IndividualSimulation individualSimulation, IPKSimProject project)
{
return(Task.Run(() =>
{
var otherSimulation = _executionContext.Clone(individualSimulation);
var individual = allTemplateBuildingBlocksFor <Individual>(otherSimulation, project).First();
var compounds = allTemplateBuildingBlocksFor <Compound>(otherSimulation, project);
otherSimulation = _simulationFactory.CreateFrom(individual, compounds, otherSimulation.ModelProperties, otherSimulation)
.DowncastTo <IndividualSimulation>();
_simulationModelCreator.CreateModelFor(otherSimulation);
_executionContext.Register(otherSimulation);
return otherSimulation;
}));
}
private async Task <ModelSimulation> createModelLessSimulationFrom(SnapshotSimulation snapshot, PKSimProject project)
{
var simulationSubject = simulationSubjectFrom(snapshot, project);
var compounds = compoundsFrom(snapshot.Compounds, project);
var modelProperties = modelPropertiesFrom(snapshot.Model, simulationSubject);
var simulation = _simulationFactory.CreateFrom(simulationSubject, compounds, modelProperties);
MapSnapshotPropertiesToModel(snapshot, simulation);
await mapCompoundProperties(simulation, snapshot.Compounds, project);
simulation.EventProperties = await mapEventProperties(snapshot.Events, project);
await updateInteractonProperties(simulation, snapshot.Interactions, project);
//Once all used building blocks have been set, we need to ensure that they are also synchronized in the simulation
updateUsedBuildingBlockInSimulation(simulation, project);
return(simulation);
}
public IMoBiSimulation CloneSimulation(IMoBiSimulation simulationToClone)
{
var buildConfig = new MoBiBuildConfiguration
{
MoleculesInfo = CloneBuidingBlockInfo(simulationToClone.MoBiBuildConfiguration.MoleculesInfo),
ReactionsInfo = CloneBuidingBlockInfo(simulationToClone.MoBiBuildConfiguration.ReactionsInfo),
SpatialStructureInfo = CloneBuidingBlockInfo(simulationToClone.MoBiBuildConfiguration.SpatialStructureInfo),
PassiveTransportsInfo = CloneBuidingBlockInfo(simulationToClone.MoBiBuildConfiguration.PassiveTransportsInfo),
ObserversInfo = CloneBuidingBlockInfo(simulationToClone.MoBiBuildConfiguration.ObserversInfo),
EventGroupsInfo = CloneBuidingBlockInfo(simulationToClone.MoBiBuildConfiguration.EventGroupsInfo),
ParameterStartValuesInfo = CloneBuidingBlockInfo(simulationToClone.MoBiBuildConfiguration.ParameterStartValuesInfo),
MoleculeStartValuesInfo = CloneBuidingBlockInfo(simulationToClone.MoBiBuildConfiguration.MoleculeStartValuesInfo),
SimulationSettingsInfo = CloneBuidingBlockInfo(simulationToClone.MoBiBuildConfiguration.SimulationSettingsInfo)
};
var model = _cloneManagerForModel.CloneModel(simulationToClone.Model);
var simulation = _simulationFactory.CreateFrom(buildConfig, model);
simulation.UpdatePropertiesFrom(simulationToClone, _cloneManagerForModel);
return(simulation);
}
