private void addReactionPartnerTo(PKSimReaction reaction, FlatReactionPartner flatReactionPartner)
{
if (flatReactionPartner.Direction.Equals(CoreConstants.ORM.PROCESS_MOLECULE_DIRECTION_MODIFIER))
{
//---- not Educt/Product, just a modifier
reaction.AddModifier(flatReactionPartner.Molecule);
return;
}
//---- from now on, must be educt/product
var reactionPartner = new ReactionPartnerBuilder()
{
MoleculeName = flatReactionPartner.Molecule,
StoichiometricCoefficient = flatReactionPartner.StoichCoeff
};
if (flatReactionPartner.Direction.Equals(CoreConstants.ORM.PROCESS_MOLECULE_DIRECTION_IN))
{
reaction.AddEduct(reactionPartner);
return;
}
if (flatReactionPartner.Direction.Equals(CoreConstants.ORM.PROCESS_MOLECULE_DIRECTION_OUT))
{
reaction.AddProduct(reactionPartner);
return;
}
//invalid direction (should never happen)
throw new ArgumentOutOfRangeException(flatReactionPartner.Direction);
}
private void addReactionPartnersTo(PKSimReaction reaction, string reactionName)
{
var allPartners = (from rp in _reactionPartnerRepository.All()
where rp.Reaction.Equals(reactionName)
select rp).ToList();
foreach (var flatReactionPartner in allPartners)
{
addReactionPartnerTo(reaction, flatReactionPartner);
}
}
protected override void Context()
{
base.Context();
_process = new EnzymaticProcess().WithName("P1");
_process.InternalName = "internalNAme";
_drug = new MoleculeBuilder().WithName("drug");
_metabolite = new MoleculeBuilder().WithName("metabolite");
_enzymeName = "P1";
_formulaCache = new FormulaCache();
_kinetic = new ExplicitFormula().WithId("trala");
_kinetic.AddObjectPath(new FormulaUsablePath(new[] { "Organism", CoreConstants.KeyWords.Molecule }));
_kinetic.AddObjectPath(new FormulaUsablePath(new[] { "Organism", CoreConstants.KeyWords.Protein }));
_parameterFormula = new ExplicitFormula();
_parameterFormula.AddObjectPath(new FormulaUsablePath(new[] { "Liver", CoreConstants.KeyWords.Molecule }));
var pkSimReaction = new PKSimReaction().WithName("template");
A.CallTo(() => _simulationActiveProcessRepository.ProcessFor <PKSimReaction>(_process.InternalName)).Returns(pkSimReaction);
pkSimReaction.Formula = _kinetic;
A.CallTo(() => _cloneManager.Clone(pkSimReaction)).Returns(pkSimReaction);
}
protected override void Context()
{
base.Context();
_formulaCache = new FormulaCache();
_protein = new MoleculeBuilder().WithName("CYP3A4");
_interactionProcess = new InductionProcess().WithName("Induction");
_interactionProcess.InternalName = "AA";
_compound = new Compound().WithName("Inhibitor");
_compound.AddProcess(_interactionProcess);
_template = new PKSimReaction();
A.CallTo(() => _simulationActiveProcessRepository.ProcessFor <PKSimReaction>(_interactionProcess.InternalName)).Returns(_template);
var reaction = new PKSimReaction {
Formula = new ExplicitFormula().WithName("ABC")
};
reaction.Formula.AddObjectPath(new FormulaUsablePath(CoreConstants.KeyWords.Protein, "P1").WithAlias("P1"));
reaction.Formula.AddObjectPath(new FormulaUsablePath(CoreConstants.KeyWords.Reaction, "R1").WithAlias("R1"));
reaction.Formula.AddObjectPath(new FormulaUsablePath(CoreConstants.KeyWords.Molecule, "M11").WithAlias("M1"));
A.CallTo(() => _cloneManager.Clone <IReactionBuilder>(_template)).Returns(reaction);
}
protected override void Because()
{
_reaction = sut.All().FirstOrDefault(r => r.Name.Equals(_reactionName1));
}
