protected override void Context()
{
base.Context();
var formula = new ExplicitFormula().WithFormulaString("123").WithName("TOTO");
formula.AddObjectPath(new FormulaUsablePath(new[] { "Organism", CoreConstants.KeyWords.Molecule }));
formula.AddObjectPath(new FormulaUsablePath(new[] { "Organism", CoreConstants.Molecule.DrugFcRnComplexTemplate }));
_reaction = new PKSimReaction().WithName("xx").WithId("xx").WithFormula(formula);
_reaction.AddEduct(new ReactionPartnerBuilder(CoreConstants.KeyWords.Molecule, 1));
_reaction.AddEduct(new ReactionPartnerBuilder("XY", 1));
_reaction.AddProduct(new ReactionPartnerBuilder(CoreConstants.Molecule.DrugFcRnComplexTemplate, 1));
_reaction.AddModifier(CoreConstants.KeyWords.Molecule);
_formulaCache = new BuildingBlockFormulaCache();
A.CallTo(() => _cloneManager.Clone(_reaction)).Returns(_reaction);
}
/// <summary>
/// Creates the Educts of the MoBi reaction.
/// </summary>
private void CreateEducts(Reaction sbmlReaction, IReactionBuilder reactionBuilder, Model model)
{
for (long i = 0; i < sbmlReaction.getNumReactants(); i++)
{
var educt = CreateReactionPartner(sbmlReaction.getReactant(i), model);
if (educt != null)
{
reactionBuilder.AddEduct(educt);
}
}
}
public override void GlobalContext()
{
base.GlobalContext();
_buildConfiguration = DomainFactoryForSpecs.CreateDefaultConfiguration();
var molecules = _buildConfiguration.Molecules;
_moleculeA = new MoleculeBuilder().WithName("A").WithDimension(DomainFactoryForSpecs.AmountDimension);
_moleculeA.DefaultStartFormula = new ConstantFormula(10);
molecules.Add(_moleculeA);
var reactions = _buildConfiguration.Reactions;
_reactionR1 = new ReactionBuilder().WithName("R1");
_reactionR1.CreateProcessRateParameter = true;
_reactionR1.Formula = new ConstantFormula(5);
_reactionR1.AddEduct(new ReactionPartnerBuilder(_moleculeA.Name, 2));
reactions.Add(_reactionR1);
_simulation = DomainFactoryForSpecs.CreateSimulationFor(_buildConfiguration);
}