public void Visit(IMoleculeBuildingBlock moleculeBuildingBlock)
{
foreach (var moleculeBuilder in moleculeBuildingBlock.Where(x => !x.ContainsName(Constants.Parameters.CONCENTRATION)).ToList())
{
var concentrationParameter = _parameterFactory.CreateConcentrationParameter(moleculeBuildingBlock.FormulaCache);
moleculeBuilder.AddParameter(concentrationParameter);
}
convertFormulaReferencingAeffIn(moleculeBuildingBlock);
}
public ValidationResult Validate(IMoleculeBuildingBlock moleculeBuildingBlock)
{
var validationResults = new ValidationResult();
foreach (var molecule in moleculeBuildingBlock.Where(m => m.IsFloating))
{
foreach (var parameter in molecule.Parameters.Where(parameterIsInvalid))
{
validationResults.AddMessage(NotificationType.Error, parameter, Error.FloatingMoleculeParameterNotDefined(molecule.Name, parameter.Name, parameter.Value), moleculeBuildingBlock);
}
}
return(validationResults);
}
private void addStandardObserversTo(Simulation simulation, IObserverBuildingBlock observerBuildingBlock, IMoleculeBuildingBlock moleculeBuildingBlock)
{
var allMoleculesNeedingConcentrationObservers = moleculeBuildingBlock.Where(concentrationIsNeeded).Select(x => x.Name).ToList();
var compoundNames = simulation.CompoundNames;
foreach (var observerTemplate in _observerBuilderRepository.AllFor(simulation.ModelProperties))
{
if (isDrugFcRnObserver(observerTemplate))
{
//special case: protein model observer for drug and its FcRn complex.
//Observer must be created separately for every drug because complexname can not be referenced in generic way by now
//E.g.: for drug C1, Observer is f("C1", "C1-FcRn_Complex"))
foreach (var compoundName in compoundNames)
{
var observer = _cloneManager.Clone(observerTemplate.ObserverBuilder, observerBuildingBlock.FormulaCache);
observer.Name = CoreConstants.Observer.ObserverNameFrom(observer.Name, compoundName);
observer.Formula.ReplaceKeywordsInObjectPaths(
new[] { CoreConstants.Molecule.DrugFcRnComplexTemplate },
new[] { CoreConstants.Molecule.DrugFcRnComplexName(compoundName) }
);
observer.AddMoleculeName(compoundName);
observerBuildingBlock.Add(observer);
}
}
else
{
var observer = _cloneManager.Clone(observerTemplate.ObserverBuilder, observerBuildingBlock.FormulaCache);
compoundNames.Each(observer.AddMoleculeName);
if (observer.IsConcentration())
{
allMoleculesNeedingConcentrationObservers.Each(observer.AddMoleculeName);
}
observerBuildingBlock.Add(observer);
}
}
}