private static MoleculeBuilder createMoleculeBuilder(string moleculeName)
{
var drug = new MoleculeBuilder().WithName(moleculeName);
drug.AddParameter(new Parameter().WithName("MoleculeProperty").WithFormula(new ConstantFormula(1)).WithMode(ParameterBuildMode.Global));
drug.AddParameter(new Parameter().WithName("NaNParameter").WithFormula(new ConstantFormula(double.NaN)).WithMode(ParameterBuildMode.Global));
return(drug);
}
public void TestSerialization()
{
MoleculeBuilder x1 = CreateObject <MoleculeBuilder>().WithName("Monica.Builder");
x1.IsFloating = true;
x1.QuantityType = QuantityType.Metabolite;
x1.DefaultStartFormula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(23.4);
TransportBuilder t1 = CreateObject <TransportBuilder>().WithName("Passive Transport");
IFormula consFormula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(5);
IParameter transporterParameter = CreateObject <Parameter>().WithName("Passive Transport Param").WithFormula(consFormula).WithMode(ParameterBuildMode.Property)
.WithDimension(DimensionLength);
t1.AddParameter(transporterParameter);
IFormula f1 = CreateObject <ExplicitFormula>().WithDimension(DimensionLength).WithFormulaString("3*Patty");
IFormulaUsablePath fup = new FormulaUsablePath(new[] { "Patricia" }).WithAlias("Patty").WithDimension(DimensionLength);
f1.AddObjectPath(fup);
IParameter p1 = CreateObject <Parameter>().WithName("Patricia").WithFormula(f1).WithValue(3.1).WithMode(ParameterBuildMode.Property);
IParameter p2 = CreateObject <Parameter>().WithName("Pascal").WithFormula(f1).WithValue(3.2).WithMode(ParameterBuildMode.Local);
IParameter p3 = CreateObject <Parameter>().WithName("Paul").WithFormula(f1).WithValue(3.3);
x1.AddParameter(p1);
x1.AddParameter(p2);
var atbc1 = CreateObject <TransporterMoleculeContainer>().WithName("Tranquilo");
ITransportBuilder atb1 = CreateObject <TransportBuilder>();
atb1.Formula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(2.5);
atb1.AddParameter(p3);
atb1.Name = "Tranquilo";
atbc1.AddActiveTransportRealization(atb1);
var atbc2 = CreateObject <TransporterMoleculeContainer>().WithName("Tranquilo2");
ITransportBuilder atb2 = CreateObject <TransportBuilder>();
atb2.Formula = f1;
atb2.Name = "Tranquilo2";
atbc2.AddActiveTransportRealization(atb2);
x1.AddTransporterMoleculeContainer(atbc1);
x1.AddTransporterMoleculeContainer(atbc2);
x1.IsXenobiotic = !x1.IsXenobiotic;
var interactionContainer = CreateObject <InteractionContainer>().WithName("Interactions");
x1.AddInteractionContainer(interactionContainer);
var x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualMoleculeBuilder(x1, x2);
}
protected override void Context()
{
base.Context();
var container = new Container {
Mode = ContainerMode.Physical, Name = "containerName"
};
var subContainer = new Container {
Mode = ContainerMode.Physical, Name = "subContainerName"
};
subContainer.Add(new Parameter {
Name = "containerParameter"
});
container.Add(subContainer);
_spatialStructure.AddTopContainer(container);
var builder = new MoleculeBuilder {
Name = "C1"
};
builder.AddParameter(new Parameter {
BuildMode = ParameterBuildMode.Local, Name = "localParameter"
});
_moleculeBuildingBlock.Add(builder);
}
protected override void Context()
{
base.Context();
var builder = new MoleculeBuilder {
Name = "C1"
};
builder.AddParameter(new Parameter {
BuildMode = ParameterBuildMode.Local, Name = "localParameter"
});
_moleculeBuildingBlock.Add(builder);
}
protected override void Context()
{
_quantity = _parameter;
base.Context();
var moleculeBuilder = new MoleculeBuilder();
moleculeBuilder.AddParameter(_parameter);
var moleculeBuildingBlock = new MoleculeBuildingBlock {
moleculeBuilder
};
_buildingBlockInfo.UntypedBuildingBlock = moleculeBuildingBlock;
}
protected override void Context()
{
base.Context();
_parameter = new Parameter()
.WithName("P")
.WithMode(_parameterBuildMode)
.WithParentContainer(new Container().WithName("Drug"));
var moleculeBuilder = new MoleculeBuilder().WithName("Drug");
var parameterBuilder = new Parameter()
.WithName(_parameter.Name)
.WithMode(_parameterBuildMode);
moleculeBuilder.AddParameter(parameterBuilder);
_moleculeBuidingBlock.Add(moleculeBuilder);
}
protected override void Context()
{
base.Context();
var moleculeBuildingBlock1 = new MoleculeBuildingBlock().WithName("X");
moleculeBuildingBlock1.Version = 1;
var moleculeBuilderA = new MoleculeBuilder().WithName("MSVa");
moleculeBuilderA.AddParameter(new Parameter().WithMode(ParameterBuildMode.Local));
moleculeBuildingBlock1.Add(moleculeBuilderA);
var moleculeBuildingBlock2 = new MoleculeBuildingBlock().WithName("X");
moleculeBuildingBlock2.Version = 1;
moleculeBuilderA = new MoleculeBuilder().WithName("MSVa");
moleculeBuildingBlock2.Add(moleculeBuilderA);
_object1 = moleculeBuildingBlock1;
_object2 = moleculeBuildingBlock2;
}