private void convertIndividual(Individual individual)
{
if (individual == null)
{
return;
}
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
if (!individual.IsHuman)
{
return;
}
if (individual.Organism.Parameter(CoreConstants.Parameter.BSA) != null)
{
return;
}
var defaultHuman = _defaultIndividualRetriever.DefaultHuman();
var bsa = defaultHuman.Organism.Parameter(CoreConstants.Parameter.BSA);
individual.Organism.Add(_cloner.Clone(bsa));
}
private void updateFractionOfBloodForSampling(Individual individual)
{
var defaultHuman = _defaultIndividualRetriever.DefaultHuman();
var oneStandardFractionOfBloodParameter = defaultHuman.GetAllChildren <IParameter>(x => x.IsNamed(FRACTION_OF_BLOOD_FOR_SAMPLING)).First();
var allFractionOfBloodParameters = individual.GetAllChildren <IParameter>(x => x.IsNamed(FRACTION_OF_BLOOD_FOR_SAMPLING));
allFractionOfBloodParameters.Each(x => { x.Info.UpdatePropertiesFrom(oneStandardFractionOfBloodParameter.Info); });
}
public void Visit(Individual individual)
{
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
performCommonConversion(individual);
Visit(individual.OriginData);
foreach (var transporter in individual.AllMolecules <IndividualTransporter>().SelectMany(x => x.AllExpressionsContainers()))
{
var oldProcessNames = transporter.ProcessNames.ToList();
transporter.ClearProcessNames();
foreach (var processName in oldProcessNames)
{
transporter.AddProcessName(processName.Replace("_MM", ""));
}
}
//change container type for molecules
foreach (var molecule in individual.AllMolecules())
{
molecule.ContainerType = ContainerType.Molecule;
updateOntogeny(molecule);
}
//special parameters that need conversion by hand
convertIndividualParameters(individual.Organism);
convertIndividualForTwoPore(individual);
var human = _defaultIndividualRetriever.DefaultHuman();
individual.Organism.Add(clone(human.Organism, CoreConstants.Parameters.ONTOGENY_FACTOR_ALBUMIN));
individual.Organism.Add(clone(human.Organism, CoreConstants.Parameters.ONTOGENY_FACTOR_AGP));
individual.Organism.Add(clone(human.Organism, CoreConstants.Parameters.PLASMA_PROTEIN_SCALE_FACTOR));
if (!individual.IsHuman)
{
individual.OriginData.AddCalculationMethod(_calculationMethodRepository.FindByName("MucosaVolume_Animals"));
}
else
{
individual.OriginData.AddCalculationMethod(_calculationMethodRepository.FindByName("MucosaVolume_Human"));
individual.OriginData.GestationalAge = CoreConstants.NOT_PRETERM_GESTATIONAL_AGE_IN_WEEKS;
individual.OriginData.GestationalAgeUnit = CoreConstants.Units.Weeks;
var gestationalAge = human.Organism.Parameter(Constants.Parameters.GESTATIONAL_AGE);
if (!individual.Organism.ContainsName(Constants.Parameters.GESTATIONAL_AGE))
{
individual.Organism.Add(_cloner.Clone(gestationalAge));
}
}
}
private void addFractionEndosomalParametersTo(Individual individual)
{
var defaultHuman = _defaultIndividualRetriever.DefaultHuman();
var allFractionEndosomalParameters =
defaultHuman.GetAllChildren <IParameter>(x => x.IsNamed(FRACTION_ENDOSOMAL));
allFractionEndosomalParameters.Each(x =>
{
//Find container in the individual to convert
var containerPath = new ObjectPath(x.ParentContainer.ConsolidatedPath());
var container = individual.Root.EntityAt <IContainer>(containerPath);
//add clone of parameter
container.Add(_cloner.Clone(x));
});
}
private void exportToFolder(string exportFolder)
{
var defaultIndividual = _defaultIndividualRetriever.DefaultHuman();
var batchSimulation = new Simulation();
batchSimulation.Individual = new Individual
{
Age = defaultIndividual.Age,
Height = defaultIndividual.MeanHeight,
Species = defaultIndividual.Species.Name,
Population = defaultIndividual.Population.Name,
};
batchSimulation.Compounds.Add(new Compound {
Name = "Standard Molecule", Lipophilicity = 3, FractionUnbound = 0.1, MolWeight = 4E-7, SolubilityAtRefpH = 9999, RefpH = 7
});
var intrevanousBolus = new ApplicationProtocol {
CompoundName = "Standard Molecule", ApplicationType = CoreConstants.Application.Name.IntravenousBolus, Dose = 1, DoseUnit = "mg/kg", DosingInterval = DosingIntervals.Single.ToString()
};
batchSimulation.Configuration = new SimulationConfiguration {
Model = CoreConstants.Model.FourComp
};
batchSimulation.ApplicationProtocols.Add(intrevanousBolus);
var fourCompIvBolusMgPerKg = configurationFrom(batchSimulation);
batchSimulation.Configuration = new SimulationConfiguration {
Model = CoreConstants.Model.TwoPores
};
var twoPore = configurationFrom(batchSimulation);
batchSimulation.ApplicationProtocols.Clear();
intrevanousBolus.DoseUnit = "mg";
batchSimulation.ApplicationProtocols.Add(intrevanousBolus);
batchSimulation.Configuration = new SimulationConfiguration {
Model = CoreConstants.Model.FourComp
};
var fourCompIvBolusMg = configurationFrom(batchSimulation);
twoPore.SpatialStructure.Name = "Human 2 Pores";
twoPore.PassiveTransports.Name = "2 Pores Passive Transports";
fourCompIvBolusMgPerKg.SpatialStructure.Name = "Human Standard";
fourCompIvBolusMgPerKg.PassiveTransports.Name = "Standard Passive Transports";
fourCompIvBolusMgPerKg.EventGroups.Name = "IV Bolus";
fourCompIvBolusMgPerKg.Molecules.Name = "Standard Molecule";
fourCompIvBolusMgPerKg.Observers.Name = "Standard Observer";
fourCompIvBolusMg.EventGroups.Name = "IV Bolus (mg)";
var defaultCompound = fourCompIvBolusMgPerKg.Molecules.First();
defaultCompound.Name = string.Empty;
defaultCompound.Parameter(CoreConstants.Parameter.LIPOPHILICITY).Value = double.NaN;
defaultCompound.Parameter(CoreConstants.Parameter.MOLECULAR_WEIGHT).Value = double.NaN;
defaultCompound.Parameter(CoreConstants.Parameter.FractionUnbound).Value = double.NaN;
defaultCompound.Parameter(CoreConstants.Parameter.SolubilityAtRefpH).Value = double.NaN;
_moBiExportTask.UpdateObserverForAllFlag(fourCompIvBolusMgPerKg.Observers);
var buildingBlocks = new IBuildingBlock[]
{
twoPore.SpatialStructure, twoPore.PassiveTransports,
fourCompIvBolusMgPerKg.SpatialStructure, fourCompIvBolusMgPerKg.PassiveTransports, fourCompIvBolusMgPerKg.EventGroups, fourCompIvBolusMgPerKg.Molecules, fourCompIvBolusMgPerKg.Observers,
fourCompIvBolusMg.EventGroups
};
buildingBlocks.Each(bb => saveToPKML(bb, exportFolder));
}
