private void addIrreversibleBindings(IMoleculeBuilder molecule, InteractionProcess irreversibleInteraction)
{
var irreversibleBindingReaction = _processBuilderMapper.InactivationReactionFrom(irreversibleInteraction, molecule, _allMoleculeNames, _reactionBuildingBlock.FormulaCache);
_interactionKineticUpdater.UpdateReaction(irreversibleBindingReaction, molecule.Name, irreversibleInteraction.ParentCompound.Name, _simulation, _reactionBuildingBlock.FormulaCache);
_reactionBuildingBlock.Add(irreversibleBindingReaction);
}
private void addInduction(IMoleculeBuilder molecule, InteractionProcess inductionProcess)
{
var inductionReaction =
_processBuilderMapper.InductionReactionFrom(inductionProcess, molecule, _allMoleculeNames, _reactionBuildingBlock.FormulaCache);
_reactionBuildingBlock.Add(inductionReaction);
}
public IReactionBuilder InductionReactionFrom(InteractionProcess interactionProcess, IMoleculeBuilder protein, IReadOnlyCollection <string> forbiddenNames, IFormulaCache formulaCache)
{
var reaction = interactionReactionFrom(interactionProcess, protein, forbiddenNames, formulaCache);
reaction.AddProduct(new ReactionPartnerBuilder(protein.Name, 1));
return(reaction);
}
protected override void Context()
{
base.Context();
_compound = new Compound().WithName("Comp");
_interactionProcess = new InhibitionProcess {
ParentContainer = _compound
}.WithName("Proc");
}
private IReactionBuilder interactionReactionFrom(InteractionProcess interactionProcess, IMoleculeBuilder protein, IReadOnlyCollection <string> forbiddenNames, IFormulaCache formulaCache)
{
var compound = interactionProcess.ParentCompound;
var reactionName = CoreConstants.CompositeNameFor(compound.Name, interactionProcess.Name);
var reaction = createReactionFromProcess(interactionProcess, reactionName, forbiddenNames);
//replace keywords
replaceKeywordsInProcess(reaction, new[] { CoreConstants.KeyWords.Molecule, CoreConstants.KeyWords.Protein, CoreConstants.KeyWords.Reaction },
new[] { compound.Name, protein.Name, interactionProcess.Name });
formulaCache.Add(reaction.Formula);
return(reaction);
}
public IReactionBuilder InductionReactionFrom(InteractionProcess interactionProcess, IMoleculeBuilder protein,
IReadOnlyCollection <string> forbiddenNames, IFormulaCache formulaCache)
{
var reaction = interactionReactionFrom(interactionProcess, protein, forbiddenNames, formulaCache);
reaction.AddProduct(new ReactionPartnerBuilder(protein.Name, 1));
//Induction occurs only in Intracellular and Interstitial
reaction.ContainerCriteria.Add(new InContainerCondition(TISSUE_ORGAN));
reaction.ContainerCriteria.Add(new NotMatchTagCondition(PLASMA));
reaction.ContainerCriteria.Add(new NotMatchTagCondition(BLOOD_CELLS));
reaction.ContainerCriteria.Add(new NotMatchTagCondition(ENDOSOME));
return(reaction);
}
protected override void Context()
{
_partialProcessRetriever = new PartialProcessRetriever();
_individual = new Individual();
_simulation = A.Fake <Simulation>();
_compound = new Compound().WithName("Comp");
_notSelectedInteractionProcess = A.Fake <InteractionProcess>();
A.CallTo(() => _simulation.Individual).Returns(_individual);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound });
sut = new InteractionProcessRetriever(_partialProcessRetriever)
{
NotSelectedInteractionProcess = _notSelectedInteractionProcess
};
}
protected override void Context()
{
_interactionProcessRetriever = A.Fake <IInteractionProcessRetriever>();
_view = A.Fake <ISimulationCompoundInteractionSelectionView>();
sut = new SimulationCompoundInteractionSelectionPresenter(_view, _interactionProcessRetriever);
_interactionProperties = new InteractionProperties();
_allSimulationInteractionProcesses = new List <SimulationPartialProcess>();
_simulation = A.Fake <Simulation>();
var individual = new Individual().WithName("Enzyme");
_molecule1 = new IndividualEnzyme().WithName("CYP3A4");
_undefinedLiver = new IndividualEnzyme().WithName(CoreConstants.Molecule.UndefinedLiver);
individual.AddMolecule(_molecule1);
individual.AddMolecule(_undefinedLiver);
_interactionProcess1 = new InhibitionProcess().WithName("INTERACTION1");
_interactionProcess2 = new InhibitionProcess().WithName("INTERACTION2");
_interactionProcess3 = new InhibitionProcess().WithName("INTERACTION3");
var comp1 = new Compound();
comp1.AddProcess(_interactionProcess1);
var comp2 = new Compound();
comp2.AddProcess(_interactionProcess2);
comp2.AddProcess(_interactionProcess3);
_allSimulationInteractionProcesses.Add(new SimulationPartialProcess {
CompoundProcess = _interactionProcess1, IndividualMolecule = _molecule1
});
_allSimulationInteractionProcesses.Add(new SimulationPartialProcess {
CompoundProcess = _interactionProcess2, IndividualMolecule = _molecule1
});
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Individual).Returns(individual);
A.CallTo(() => _simulation.Compounds).Returns(new[] { comp1, comp2 });
A.CallTo(_interactionProcessRetriever).WithReturnType <IReadOnlyList <SimulationPartialProcess> >()
.Invokes(x => _useDefaultMap = x.GetArgument <bool>(2))
.Returns(_allSimulationInteractionProcesses);
A.CallTo(() => _view.BindTo(A <IEnumerable <SimulationInteractionProcessSelectionDTO> > ._))
.Invokes(x => _allSimulationInteractionProcessSelectionDTO = x.GetArgument <IEnumerable <SimulationInteractionProcessSelectionDTO> >(0));
}
protected override void Context()
{
_simulation = A.Fake <Simulation>();
_competitiveInhibition1 = new InhibitionProcess {
InteractionType = InteractionType.CompetitiveInhibition
}.WithName("CompetitiveInhibition1");
_competitiveInhibition2 = new InhibitionProcess {
InteractionType = InteractionType.CompetitiveInhibition
}.WithName("CompetitiveInhibition2");
_uncompetitiveInhibition = new InhibitionProcess {
InteractionType = InteractionType.UncompetitiveInhibition
}.WithName("UncompetitiveInhibition");
_compound1 = new Compound().WithName("Compound1");
_compound1.AddProcess(_competitiveInhibition1);
_compound1.AddProcess(_uncompetitiveInhibition);
_compound2 = new Compound().WithName("Compound2");
_compound2.AddProcess(_competitiveInhibition2);
_interactionProperties = new InteractionProperties();
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound1, _compound2 });
_objectPathFactory = new ObjectPathFactoryForSpecs();
_dimensionRepository = A.Fake <IDimensionRepository>();
_interactionTask = new InteractionTask();
sut = new CompetitiveInhibitionsKineticUpdaterSpecification(_objectPathFactory, _dimensionRepository, _interactionTask);
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _competitiveInhibition1.Name, CompoundName = _compound1.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _competitiveInhibition2.Name, CompoundName = _compound2.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _uncompetitiveInhibition.Name, CompoundName = _compound2.Name
});
}
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);
}
private static bool shouldGenerateInteractionContainer(InteractionProperties interactionProperties, InteractionProcess interactionProcess)
{
return(interactionProperties.Uses(interactionProcess));
}
private IFormulaUsablePath kiPath(string kiParameter, Compound inhibitor, InteractionProcess process, string kiAlias)
{
return(_objectPathFactory.CreateFormulaUsablePathFrom(inhibitor.Name, process.Name, kiParameter)
.WithAlias(kiAlias)
.WithDimension(_dimensionRepository.MolarConcentration));
}
protected override void Context()
{
base.Context();
_interactionProcess = new InhibitionProcess();
}