private void fillReactions()
{
foreach (var flatProc in _flatProcessesRepository.All().Where(processIsNonTemplateReaction))
{
_allReactions.Add(_activeProcessMapper.MapFrom(flatProc).DowncastTo <PKSimReaction>());
}
_allReactions.Each(process => _parameterContainerTask.AddProcessBuilderParametersTo(process));
}
protected override void DoStart()
{
var query = _flatProcessesRepository.All().Where(processIsSimulationActiveProcess)
.MapAllUsing(_activeProcessMapper)
.Where(activeProcess => activeProcess != null);
_allSimulationActiveProcesses.AddRange(query);
_allSimulationActiveProcesses.Each(process => _parameterContainerTask.AddProcessBuilderParametersTo(process));
}
public PKSimTransport MapFrom(FlatProcess flatProcess)
{
var transport = _entityBaseFactory.Create <PKSimTransport>()
.WithName(flatProcess.Name)
.WithDimension(_dimensionRepository.AmountPerTime);
_parameterContainerTask.AddProcessBuilderParametersTo(transport);
addDescriptorConditions(transport.SourceCriteria, ProcessTagType.Source, transport.Name);
addDescriptorConditions(transport.TargetCriteria, ProcessTagType.Target, transport.Name);
transport.CalculationMethod = flatProcess.CalculationMethod;
transport.Rate = flatProcess.Rate;
transport.Formula = _formulaFactory.RateFor(transport, new FormulaCache());
transport.CreateProcessRateParameter = flatProcess.CreateProcessRateParameter;
return(transport);
}
private void addInteractionParameters(Compound compound, IMoleculeBuilder drug, InteractionProperties interactionProperties)
{
foreach (var interactionProcess in compound.AllProcesses <InteractionProcess>())
{
if (!shouldGenerateInteractionContainer(interactionProperties, interactionProcess))
{
continue;
}
var interactionContainer = _objectBaseFactory.Create <InteractionContainer>()
.WithIcon(interactionProcess.Icon)
.WithName(interactionProcess.InternalName);
//only add global pamrameters to the intercation container
_parameterContainerTask.AddProcessBuilderParametersTo(interactionContainer);
_parameterSetUpdater.UpdateValuesByName(interactionProcess, interactionContainer);
interactionContainer.Name = interactionProcess.Name;
drug.AddInteractionContainer(interactionContainer);
}
}
public TransporterMoleculeContainer ActiveTransportFrom(CompoundProcess compoundProcess, IndividualTransporter transporter, IFormulaCache formulaCache)
{
var transporterMoleculeContainer = _objectBaseFactory.Create <TransporterMoleculeContainer>().WithName(compoundProcess.InternalName);
transporterMoleculeContainer.Icon = compoundProcess.Icon;
transporterMoleculeContainer.TransportName = compoundProcess.Name;
foreach (var inducedProcess in transporter.AllInducedProcesses())
{
var activeTransporterBuilder = activeTransportFrom(compoundProcess, inducedProcess, formulaCache);
transporterMoleculeContainer.Icon = activeTransporterBuilder.Icon;
activeTransporterBuilder.TransportType = transporter.TransportType;
transporterMoleculeContainer.AddActiveTransportRealization(activeTransporterBuilder);
updateTransporterTagsFor(transporter, activeTransporterBuilder, inducedProcess);
}
_parameterContainerTask.AddProcessBuilderParametersTo(transporterMoleculeContainer);
_parameterSetUpdater.UpdateValuesByName(compoundProcess.AllParameters(), transporterMoleculeContainer.Parameters);
transporterMoleculeContainer.Name = transporter.Name;
return(transporterMoleculeContainer);
}