private void addLocalParametersToMolecule(IModel model, IBuildConfiguration buildConfiguration)
{
// retrieve all molecules container defined int the spatial structure
var allMoleculePropertiesContainer = model.Root.GetAllChildren <IContainer>(x => x.IsNamed(Constants.MOLECULE_PROPERTIES)).ToList();
var allPresentMolecules = buildConfiguration.AllPresentXenobioticFloatingMoleculeNames().ToList();
var allEndogenous = buildConfiguration.AllPresentEndogenousStationaryMoleculeNames().ToList();
foreach (var moleculePropertiesContainer in allMoleculePropertiesContainer)
{
addLocalStructureMoleculeParametersToMoleculeAmount(allPresentMolecules, moleculePropertiesContainer, buildConfiguration, model, x => !isEdogenousParameter(x));
addLocalStructureMoleculeParametersToMoleculeAmount(allEndogenous, moleculePropertiesContainer, buildConfiguration, model, isEdogenousParameter);
// remove the molecule properties container only used as template
moleculePropertiesContainer.ParentContainer.RemoveChild(moleculePropertiesContainer);
}
}
public IContainer MapFrom(IModel model, IBuildConfiguration buildConfiguration)
{
var moleculeNames = buildConfiguration.AllPresentFloatingMoleculeNames();
var neighborhoodsParentContainer = _objectBaseFactory.Create <IContainer>()
.WithMode(ContainerMode.Logical)
.WithName(Constants.NEIGHBORHOODS);
var startValuesForFloatingMolecules = presentMoleculesCachedByContainerPath(moleculeNames, buildConfiguration);
var moleculeNamesCopyProperties = buildConfiguration.AllPresentXenobioticFloatingMoleculeNames();
buildConfiguration.SpatialStructure.Neighborhoods.Each(nb =>
neighborhoodsParentContainer.Add(_neighborhoodMapper.MapFrom(nb,
model,
buildConfiguration,
moleculeNamesFor(nb, startValuesForFloatingMolecules),
moleculeNamesCopyProperties)));
return(neighborhoodsParentContainer);
}