public override void GlobalContext()
{
base.GlobalContext();
_compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
_cloneManager = IoC.Resolve <ICloneManager>();
_liverMicrosomeFirstOrder = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_LIVER_MICROSOME_FIRST_ORDER));
_liverMicrosomeFirstOrder.Name = "liverMicrosomeFirstOrder";
_liverMicrosomeRes = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.LIVER_MICROSOME_RES));
_liverMicrosomeRes.Name = "liverMicrosomeRes";
}
public override void GlobalContext()
{
base.GlobalContext();
_compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
_cloneManager = IoC.Resolve <ICloneManager>();
_enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
_transporterFactory = IoC.Resolve <IIndividualTransporterFactory>();
_modelPropertiesTask = IoC.Resolve <IModelPropertiesTask>();
_modelConfigurationRepository = IoC.Resolve <IModelConfigurationRepository>();
_compound = DomainFactoryForSpecs.CreateStandardCompound();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_enzyme = _enzymeFactory.CreateFor(_individual).DowncastTo <IndividualEnzyme>().WithName("CYP");
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Plasma).Value = _relExpNormPls;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.BloodCells).Value = _relExpNormBloodCells;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.VascularEndothelium).Value = _relExpVascEndo;
_individual.AddMolecule(_enzyme);
_hct = _individual.Organism.Parameter(CoreConstants.Parameters.HCT).Value;
_metabolizationProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>());
_metabolizationProcess.Name = "My Partial Process";
_metabolizationProcess.Parameter(ConverterConstants.Parameter.CLspec).Value = 15;
_compound.AddProcess(_metabolizationProcess);
_simulationRunOptions = new SimulationRunOptions {
RaiseEvents = false
};
}
public override void GlobalContext()
{
base.GlobalContext();
_compoundProcessRepo = IoC.Resolve <ICompoundProcessRepository>();
_interactionTask = IoC.Resolve <IInteractionTask>();
var cloner = IoC.Resolve <ICloneManager>();
var enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
var transporterFactory = IoC.Resolve <IIndividualTransporterFactory>();
var inhibitor = DomainFactoryForSpecs.CreateStandardCompound().WithName("Inhibitor");
var protocol2 = DomainFactoryForSpecs.CreateStandardIVBolusProtocol().WithName("IV2");
var allPartialProcesses = PartialProcesses.ToList();
foreach (var metaTemplate in allPartialProcesses)
{
var moleculeName = "Molecule_" + metaTemplate.Name;
if (metaTemplate as EnzymaticProcess != null)
{
var individualProtein = enzymeFactory.CreateFor(_individual).WithName(moleculeName);
_individual.AddMolecule(individualProtein.DowncastTo <IndividualEnzyme>().WithName(moleculeName));
}
else
{
var individualProtein = transporterFactory.CreateFor(_individual).WithName(moleculeName);
_individual.AddMolecule(individualProtein.DowncastTo <IndividualTransporter>().WithName(moleculeName));
}
var process = cloner.Clone(metaTemplate).DowncastTo <PartialProcess>();
process.Name = "Process " + moleculeName;
process.MoleculeName = moleculeName;
_compound.AddProcess(process);
var inhibitionTemplate = _compoundProcessRepo.ProcessByName <InteractionProcess>(InhibitionProcessName);
var inhibitionProcess = cloner.Clone(inhibitionTemplate);
inhibitionProcess.Name = "InhibitionProcess " + moleculeName;
inhibitionProcess.MoleculeName = moleculeName;
inhibitor.AddProcess(inhibitionProcess);
}
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(
_individual, new[] { _compound, inhibitor }, new[] { _protocol, protocol2 }).DowncastTo <IndividualSimulation>();
foreach (var inhibitionProcess in inhibitor.AllProcesses <InteractionProcess>())
{
var interactionSelection = new InteractionSelection {
CompoundName = inhibitor.Name, MoleculeName = inhibitionProcess.MoleculeName, ProcessName = inhibitionProcess.Name
};
_simulation.InteractionProperties.AddInteraction(interactionSelection);
}
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
private void convertCompound(Compound compound)
{
if (compound == null)
{
return;
}
var templateCompound = _compoundFactory.Create().WithName(compound.Name);
var solubilityTable = templateCompound.Parameter(CoreConstants.Parameters.SOLUBILITY_TABLE);
compound.Add(_cloner.Clone(solubilityTable));
var solubilityGroup = compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_SOLUBILITY);
solubilityGroup.AllAlternatives.Each(x => x.Add(_cloner.Clone(solubilityTable)));
var templateParameterCache = _containerTask.CacheAllChildrenSatisfying <IParameter>(templateCompound, x => !x.IsDefault);
var compoundParameterCache = _containerTask.CacheAllChildren <IParameter>(compound);
foreach (var parameterPath in templateParameterCache.Keys)
{
setAsInput(compoundParameterCache[parameterPath]);
}
foreach (var templateAlternativeGroup in templateCompound.AllParameterAlternativeGroups())
{
var templateAlternative = templateAlternativeGroup.AllAlternatives.First();
var compoundGroup = compound.ParameterAlternativeGroup(templateAlternativeGroup.Name);
foreach (var alternative in compoundGroup.AllAlternatives)
{
updateIsInputStateByNameAndValue(alternative, templateAlternative);
}
}
foreach (var process in compound.AllProcesses())
{
var templateProcess = _compoundProcessRepository.ProcessByName(process.InternalName);
updateIsInputStateByNameAndValue(process, templateProcess);
}
_converted = true;
}
private TProcess retrieveProcessFrom <TProcess>(CompoundProcess batchCompoundProcess) where TProcess : Model.CompoundProcess
{
var template = _compoundProcessRepository.ProcessByName <TProcess>(batchCompoundProcess.InternalName);
if (template == null)
{
_batchLogger.AddWarning($"Could not find process named '{batchCompoundProcess.InternalName}' in database");
return(null);
}
var process = _cloner.Clone(template);
process.DataSource = batchCompoundProcess.DataSource;
if (template.IsAnImplementationOf <ISpeciesDependentCompoundProcess>())
{
updateSpeciesDependentParameter(process, batchCompoundProcess);
}
updateProcessParameters(process, batchCompoundProcess);
return(process);
}
private async Task <ModelCompoundProcess> retrieveProcessFrom(CompoundProcess snapshot, SnapshotContext snapshotContext)
{
var template = _compoundProcessRepository.ProcessByName(snapshot.InternalName);
if (template == null)
{
_logger.AddError(PKSimConstants.Error.SnapshotProcessNameNotFound(snapshot.InternalName));
return(null);
}
var process = _cloner.Clone(template);
process.DataSource = snapshot.DataSource;
if (process.IsAnImplementationOf <ISpeciesDependentCompoundProcess>())
{
updateSpeciesDependentParameter(process, snapshot);
}
await UpdateParametersFromSnapshot(snapshot, process, snapshotContext, process.InternalName);
return(process);
}
