public void should_add_the_concentration_parameter_to_the_created_molecule_builder_as_a_local_parameter()
{
var param = _result.Parameter(CoreConstants.Parameters.CONCENTRATION);
param.ShouldNotBeNull();
param.BuildMode.ShouldBeEqualTo(ParameterBuildMode.Local);
}
public void should_override_the_parameters_define_as_formula()
{
var permParameter = _molecule.Parameter(CoreConstants.Parameters.PERMEABILITY);
permParameter.IsFixedValue.ShouldBeFalse();
permParameter.Formula.ShouldBeAnInstanceOf <ConstantFormula>();
permParameter.Value.ShouldBeEqualTo(_alternativePerm2.Parameter(CoreConstants.Parameters.PERMEABILITY).Value);
}
public void should_let_the_parameter_defined_as_formula_untouched_but_not_editable()
{
var permParameter = _molecule.Parameter(CoreConstants.Parameters.PERMEABILITY);
permParameter.IsFixedValue.ShouldBeFalse();
permParameter.Formula.ShouldBeAnInstanceOf <ExplicitFormula>();
permParameter.Editable.ShouldBeFalse();
}
private void updateAlternativeParameters(ParameterAlternative alternative, IMoleculeBuilder drug)
{
var allParameters = alternative.AllParameters().ToList();
foreach (var alternativeParameter in allParameters)
{
//Parameter does not exist in drug?
var drugParameter = drug.Parameter(alternativeParameter.Name);
if (drugParameter == null)
{
continue;
}
//parameter is a rate. parameter in molecule should be readonly
if (!alternativeParameter.Formula.IsConstant())
{
drugParameter.Editable = false;
}
//target parameter is a rate and source parmaeter is constant
else if (!drugParameter.Formula.IsConstant())
{
drugParameter.Formula = _objectBaseFactory.Create <ConstantFormula>().WithValue(alternativeParameter.Value);
}
_parameterSetUpdater.UpdateValue(alternativeParameter, drugParameter);
//only update value description if the alternative contains one and one only parameter
if (allParameters.Count == 1)
{
drugParameter.ValueDescription = alternative.Description;
}
}
}
private void removeGlobalExpressionsParameterFor(IMoleculeBuilder molecule)
{
CoreConstants.Parameters.AllGlobalRelExpParameters.Each(parameterName =>
{
var parameter = molecule.Parameter(parameterName);
if (parameter != null)
{
molecule.RemoveChild(parameter);
}
});
}
private void addDrugParametersTo(IMoleculeBuilder molecule, IFormulaCache formulaCache)
{
var allExistingParameters = molecule.AllParameters().ToList();
molecule.Name = CoreConstants.Molecule.Drug;
_parameterContainerTask.AddMoleculeParametersTo(molecule, formulaCache);
foreach (var parameter in molecule.AllParameters().Where(p => !allExistingParameters.Contains(p)))
{
parameter.BuildingBlockType = PKSimBuildingBlockType.Simulation;
parameter.Visible = false;
parameter.CanBeVariedInPopulation = false;
molecule.Add(parameter);
}
setDefaultParameterValues(molecule);
//default value for floating in lumen should be 0
molecule.Parameter(CoreConstants.Parameter.IS_FLOATING_IN_LUMEN).Value = 0;
}
private void updateAlternativeParameters(ParameterAlternative alternative, IMoleculeBuilder drug, IFormulaCache formulaCache)
{
var allParameters = alternative.AllParameters().ToList();
foreach (var alternativeParameter in allParameters)
{
//Parameter does not exist in drug?
var drugParameter = drug.Parameter(alternativeParameter.Name);
if (drugParameter == null)
{
continue;
}
if (alternativeParameter.Formula.IsTable())
{
var tableFormula = _cloner.Clone(alternativeParameter.Formula);
formulaCache.Add(tableFormula);
drugParameter.Formula = tableFormula;
}
//parameter is a rate. parameter in molecule should be readonly
else if (!alternativeParameter.Formula.IsConstant())
{
drugParameter.Editable = false;
}
//target parameter is a rate and source parameter is constant
else if (!drugParameter.Formula.IsConstant())
{
drugParameter.Formula = _objectBaseFactory.Create <ConstantFormula>().WithValue(alternativeParameter.Value);
}
_parameterSetUpdater.UpdateValue(alternativeParameter, drugParameter);
//Default parameter Default and visible may not match database default and need to be set according to alternative parameter
drugParameter.IsDefault = alternativeParameter.IsDefault;
drugParameter.Visible = alternativeParameter.Visible;
}
}
public void should_update_the_molecule_weight_of_all_concentration_columns_related_to_a_molecule_with_a_mol_weight_parameter()
{
_concentrationColumn.DataInfo.MolWeight.ShouldBeEqualTo(_drug.Parameter(AppConstants.Parameters.MOLECULAR_WEIGHT).Value);
_fractionColumn.DataInfo.MolWeight.ShouldBeNull();
}
public void should_remove_the_global_relative_expression_paramters_that_do_not_make_sense_for_trnasporter()
{
CoreConstants.Parameters.AllGlobalRelExpParameters.Each(parmaterName => _result.Parameter(parmaterName).ShouldBeNull());
}
public void should_set_the_default_values_of_all_default_parameter_into_the_molecule_that_where_fixed_by_the_user()
{
_molecule.Parameter(Constants.Parameters.MOL_WEIGHT).Value.ShouldBeEqualTo(_compound.Parameter(Constants.Parameters.MOL_WEIGHT).Value);
}