protected override void Context()
{
_simulation = BatchToolFactoryForSpecs.DefaultSimulation();
_settings = new JsonSerializerSettings {
NullValueHandling = NullValueHandling.Ignore
};
}
public static Simulation SimulationFrom(Individual individual, Compound compound,
ApplicationProtocol protocol, SimulationConfiguration configuration, IEnumerable <ParameterVariationSet> parameterVariationSets)
{
var simulation = new Simulation {
Individual = individual
};
simulation.Compounds.Add(compound);
simulation.ApplicationProtocols.Add(protocol);
simulation.Configuration = configuration;
simulation.ParameterVariationSets = new List <ParameterVariationSet>(parameterVariationSets);
return(simulation);
}
protected override void Context()
{
_simulation = BatchToolFactoryForSpecs.DefaultSimulation();
var pv1 = new ParameterVariationSet {
Name = "PV1"
};
pv1.ParameterValues.Add(new ParameterValue("A|B|C", 15, 0.2));
pv1.ParameterValues.Add(new ParameterValue("A|B|C|D", 20, 0.6));
_simulation.ParameterVariationSets.Add(pv1);
_settings = new JsonSerializerSettings {
NullValueHandling = NullValueHandling.Ignore
};
}
protected override void Because()
{
string output = JsonConvert.SerializeObject(_simulation, _settings);
_converted = JsonConvert.DeserializeObject <Simulation>(output);
}
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));
}
private IBuildConfiguration configurationFrom(Simulation batchSimulation)
{
return(_buildConfigurationTask.CreateFor(_simulationMapper.MapFrom(batchSimulation).Simulation, shouldValidate: false, createAgingDataInSimulation: false));
}