public void should_have_converted_the_mol_weight_of_the_compound_in_the_building_block_and_in_the_simulation()
{
_compound.Parameter(Constants.Parameters.MOL_WEIGHT).ValueInDisplayUnit.ShouldBeEqualTo(250, 1e-2);
var simCompound = _simulation.BuildingBlock <Compound>();
simCompound.Parameter(Constants.Parameters.MOL_WEIGHT).ValueInDisplayUnit.ShouldBeEqualTo(250, 1e-2);
var modelComp = _simulation.Model.Root.Container(_compound.Name);
modelComp.Parameter(Constants.Parameters.MOL_WEIGHT).ValueInDisplayUnit.ShouldBeEqualTo(250, 1e-2);
}
protected override void Context()
{
base.Context();
_formulaCache = new FormulaCache();
_compoundFactory = IoC.Resolve <ICompoundFactory>();
_parameterAlternativeFactory = IoC.Resolve <IParameterAlternativeFactory>();
_compound = _compoundFactory.Create().WithName("Comp");
_compound.Parameter(Constants.Parameters.MOL_WEIGHT).Value = 250;
//Two simple parameters without alternatives
//one parameter defined as a constant for which an alternative was also specififed
var lipoGroup = _compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY);
_alternativeLipo1 = _parameterAlternativeFactory.CreateAlternativeFor(lipoGroup).WithName("ALT_LIPO1").WithId("ALT_LIPO1");
_alternativeLipo1.Parameter(CoreConstants.Parameters.LIPOPHILICITY).Value = 2;
_alternativeLipo2 = _parameterAlternativeFactory.CreateAlternativeFor(lipoGroup).WithName("ALT_LIPO2").WithId("ALT_LIPO2");
_alternativeLipo2.Parameter(CoreConstants.Parameters.LIPOPHILICITY).Value = 5;
lipoGroup.AddAlternative(_alternativeLipo1);
lipoGroup.AddAlternative(_alternativeLipo2);
//one parameter defined as a formula with a default calculated alternative
var permAlternativeGroup = _compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_PERMEABILITY);
//value cannot be changed by user
_alternativePerm1 = _parameterAlternativeFactory.CreateDefaultAlternativeFor(permAlternativeGroup).WithName("ALT_PERM1").WithId("ALT_PERM1");
_alternativePerm2 = _parameterAlternativeFactory.CreateAlternativeFor(permAlternativeGroup).WithName("ALT_PERM2").WithId("ALT_PERM2");
_alternativePerm2.Parameter(CoreConstants.Parameters.PERMEABILITY).Value = 10;
permAlternativeGroup.AddAlternative(_alternativePerm1);
permAlternativeGroup.AddAlternative(_alternativePerm2);
}
private void checkIsDefaultFlagIn(Compound compound)
{
compound.Parameter(CoreConstants.Parameters.MOLECULAR_WEIGHT).IsDefault.ShouldBeFalse();
var lipoGroup = compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY);
var parameters = lipoGroup.AllAlternatives.Select(x => x.Parameter(CoreConstants.Parameters.LIPOPHILICITY));
parameters.Each(p => p.IsDefault.ShouldBeFalse());
}
public override void EditCompound(Compound compound)
{
_parameter = compound.Parameter(CoreConstants.Parameter.IS_SMALL_MOLECULE);
var info = _representationInfoRepository.InfoFor(_parameter);
var isSmallMolecule = new IsSmallMoleculeDTO {
Value = _parameter.Value == 1, Description = info.Description, Display = info.DisplayName
};
_view.BindTo(isSmallMolecule);
}
private void verifyEnableSaturationParameter(Compound compound)
{
compound.SupersaturationEnabled.ShouldBeFalse();
var enableSaturation = compound.Parameter(Constants.Parameters.ENABLE_SUPERSATURATION);
enableSaturation.CanBeVaried.ShouldBeTrue();
enableSaturation.Info.ReadOnly.ShouldBeFalse();
enableSaturation.Visible.ShouldBeTrue();
enableSaturation.CanBeVariedInPopulation.ShouldBeFalse();
enableSaturation.IsDefault.ShouldBeTrue();
}
public void Visit(Compound compound)
{
//required for wrong conversion between 5.1 and 5.2.1
var oldFractionUnbound = compound.Parameter(ConverterConstants.Parameter.FractionUnboundPlasma);
if (oldFractionUnbound == null)
{
return;
}
oldFractionUnbound.Name = CoreConstants.Parameter.FractionUnbound;
}
public void Visit(Compound compound)
{
//required for wrong conversion between 5.1 and 5.2.1
var oldFractionUnbound = compound.Parameter(ConverterConstants.Parameter.FractionUnboundPlasma);
if (oldFractionUnbound == null)
{
return;
}
oldFractionUnbound.Name = CoreConstants.Parameters.FRACTION_UNBOUND_PLASMA_REFERENCE_VALUE;
_converted = true;
}
public TableFormula SolubilityTableForPh(ParameterAlternative solubilityAlternative, Compound compound)
{
//Sol(pH) = ref_Solubility * Solubility_Factor (ref_pH) / Solubility_Factor(pH)
//Solubility_pKa_pH_Factor
var refPh = solubilityAlternative.Parameter(CoreConstants.Parameter.RefpH);
var refSolubility = solubilityAlternative.Parameter(CoreConstants.Parameter.SolubilityAtRefpH);
var gainPerCharge = solubilityAlternative.Parameter(CoreConstants.Parameter.SolubilityGainPerCharge);
var refSolubilityValue = refSolubility.Value;
var formula = _formulaFactory.CreateTableFormula()
.WithName(PKSimConstants.UI.Solubility)
.InitializedWith(PKSimConstants.UI.pH, PKSimConstants.UI.Solubility, refPh.Dimension, refSolubility.Dimension);
compound.Parameter(CoreConstants.Parameter.RefpH).Value = refPh.Value;
compound.Parameter(CoreConstants.Parameter.SolubilityGainPerCharge).Value = gainPerCharge.Value;
double solFactorRefpH = compound.Parameter(CoreConstants.Parameter.SOLUBILITY_P_KA__P_H_FACTOR).Value;
var allPh = new List <double>();
int ph = 0;
while (ph <= 13)
{
allPh.AddRange(new[] { ph, ph + 0.5 });
ph++;
}
allPh.Add(14);
foreach (var pH in allPh)
{
compound.Parameter(CoreConstants.Parameter.RefpH).Value = pH;
double solFactorAtpH = compound.Parameter(CoreConstants.Parameter.SOLUBILITY_P_KA__P_H_FACTOR).Value;
formula.AddPoint(pH, refSolubilityValue * solFactorRefpH / solFactorAtpH);
}
return(formula);
}
private void addNewParameters(Compound compound)
{
var defaultCompound = _compoundFactory.Create();
var plasmaProteinBindingPartner = _cloner.Clone(defaultCompound.Parameter(Constants.Parameters.PLASMA_PROTEIN_BINDING_PARTNER));
plasmaProteinBindingPartner.Value = (int)PlasmaProteinBindingPartner.Unknown;
compound.Add(plasmaProteinBindingPartner);
compound.Add(_cloner.Clone(defaultCompound.Parameter(ConverterConstants.Parameter.Kass_FcRn)));
compound.Add(_cloner.Clone(defaultCompound.Parameter(ConverterConstants.Parameter.Kd_FcRn_pls_int)));
compound.Add(_cloner.Clone(defaultCompound.Parameter(ConverterConstants.Parameter.BP_AGP)));
compound.Add(_cloner.Clone(defaultCompound.Parameter(ConverterConstants.Parameter.BP_ALBUMIN)));
compound.Add(_cloner.Clone(defaultCompound.Parameter(ConverterConstants.Parameter.BP_UNKNOWN)));
var oldKdFCRn = compound.Parameter("Kd (FcRn)");
oldKdFCRn.Name = ConverterConstants.Parameter.Kd_FcRn_Endo;
}
public void UpdateGainPerChargeInAlternatives(Compound compound, bool updateValues = true)
{
var gainPerCharge = compound.Parameter(CoreConstants.Parameter.SolubilityGainPerCharge);
gainPerCharge.GroupName = CoreConstants.Groups.COMPOUND_SOLUBILITY;
var solGroup = compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_SOLUBILITY);
foreach (var alternative in solGroup.AllAlternatives)
{
var alternativeParameter = alternative.Parameter(CoreConstants.Parameter.SolubilityGainPerCharge);
if (alternativeParameter != null)
{
if (updateValues)
{
alternativeParameter.Value = gainPerCharge.Value;
}
}
else
{
alternative.Add(_cloner.Clone(gainPerCharge));
}
}
}
public override void EditCompound(Compound compound)
{
_plasmaProteinPartner = compound.Parameter(Constants.Parameters.PLASMA_PROTEIN_BINDING_PARTNER);
base.EditCompound(compound);
}
private void convertCompound(Compound compound)
{
compound.Parameter(Constants.Parameters.MOL_WEIGHT).CanBeVaried = false;
}
public void should_have_added_the_plasma_protein_binding_partner_parameter()
{
_compound.Parameter(CoreConstants.Parameter.PLASMA_PROTEIN_BINDING_PARTNER).ShouldNotBeNull();
_compound.Parameter(CoreConstants.Parameter.PLASMA_PROTEIN_BINDING_PARTNER).Value.ShouldBeEqualTo((double)PlasmaProteinPartner.Unknown);
}
private IEnumerable <IParameter> permeabilityParametersFor(Compound compound, string permeabilityParameterName)
{
//create a temp compound from the compound factory
//retrieve the lipophilicity alternatives
var lipophilicityGroup = compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY);
foreach (var alternative in lipophilicityGroup.AllAlternatives)
{
var tempCompound = _compoundFactory.Create();
tempCompound.Parameter(Constants.Parameters.IS_SMALL_MOLECULE).Value = compound.Parameter(Constants.Parameters.IS_SMALL_MOLECULE).Value;
tempCompound.Parameter(CoreConstants.Parameters.EFFECTIVE_MOLECULAR_WEIGHT).Value = compound.Parameter(CoreConstants.Parameters.EFFECTIVE_MOLECULAR_WEIGHT).Value;
tempCompound.Parameter(CoreConstants.Parameters.LIPOPHILICITY).Value = alternative.Parameter(CoreConstants.Parameters.LIPOPHILICITY).Value;
var permParameter = tempCompound.Parameter(permeabilityParameterName);
permParameter.Editable = false;
permParameter.Name = alternative.Name;
yield return(permParameter);
}
}