public void PrepareSolubilityAlternativeForTableSolubility(ParameterAlternative solubilityAlternative)
{
var solubilityAtRefPhParameter = solubilityAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_AT_REFERENCE_PH);
var phParameter = solubilityAlternative.Parameter(CoreConstants.Parameters.REFERENCE_PH);
var solubilityGainParameter = solubilityAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_GAIN_PER_CHARGE);
resetParameters(solubilityGainParameter, solubilityAtRefPhParameter, phParameter);
solubilityAtRefPhParameter.Value = 0;
var tableParameter = solubilityAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_TABLE);
tableParameter.Visible = true;
tableParameter.IsDefault = false;
}
public SolubilityAlternativeDTO MapFrom(ParameterAlternative parameterAlternative)
{
var solubilityAlternativeDTO = new SolubilityAlternativeDTO(parameterAlternative);
var solubility = parameterAlternative.Parameter(CoreConstants.Parameter.SolubilityAtRefpH);
var refPh = parameterAlternative.Parameter(CoreConstants.Parameter.RefpH);
var gainPerCharge = parameterAlternative.Parameter(CoreConstants.Parameter.SolubilityGainPerCharge);
solubilityAlternativeDTO.SolubilityParameter = _parameterDTOMapper.MapFrom(solubility, solubilityAlternativeDTO, dto => dto.Solubility, dto => dto.SolubilityParameter);
solubilityAlternativeDTO.RefpHParameter = _parameterDTOMapper.MapFrom(refPh, solubilityAlternativeDTO, dto => dto.RefpH, dto => dto.RefpHParameter);
solubilityAlternativeDTO.GainPerChargeParameter = _parameterDTOMapper.MapFrom(gainPerCharge, solubilityAlternativeDTO, dto => dto.GainPerCharge, dto => dto.GainPerChargeParameter);
return(solubilityAlternativeDTO);
}
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);
}
public PermeabilityAlternativeDTO MapFrom(ParameterAlternative parameterAlternative, string parameterName)
{
var permeability = parameterAlternative.Parameter(parameterName);
var permeabilityAlternativeDTO = new PermeabilityAlternativeDTO(parameterAlternative, permeability.ValueOrigin);
permeabilityAlternativeDTO.PermeabilityParameter = _parameterDTOMapper.MapFrom(permeability, permeabilityAlternativeDTO, dto => dto.Permeability, dto => dto.PermeabilityParameter);
return(permeabilityAlternativeDTO);
}
public LipophilictyAlternativeDTO MapFrom(ParameterAlternative parameterAlternative)
{
var lipophilicity = parameterAlternative.Parameter(CoreConstants.Parameters.LIPOPHILICITY);
var lipophilictyAlternativeDTO = new LipophilictyAlternativeDTO(parameterAlternative, lipophilicity.ValueOrigin);
lipophilictyAlternativeDTO.LipophilictyParameter = _parameterDTOMapper.MapFrom(lipophilicity, lipophilictyAlternativeDTO, dto => dto.Lipophilicty, dto => dto.LipophilictyParameter);
return(lipophilictyAlternativeDTO);
}
public TableFormula SolubilityTableForPh(ParameterAlternative solubilityAlternative, Compound compound)
{
//Already a table formula. Use as IS!
var tableSolubility = solubilityAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_TABLE);
if (tableSolubility.Formula.IsTable())
{
return(tableSolubility.Formula.DowncastTo <TableFormula>());
}
//Sol(pH) = ref_Solubility * Solubility_Factor (ref_pH) / Solubility_Factor(pH)
//Solubility_pKa_pH_Factor
var refSolubility = solubilityAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_AT_REFERENCE_PH);
var refPh = solubilityAlternative.Parameter(CoreConstants.Parameters.REFERENCE_PH);
var gainPerCharge = solubilityAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_GAIN_PER_CHARGE);
var refSolubilityValue = refSolubility.Value;
var compoundForCalculation = _executionContext.Clone(compound);
var formula = initializeSolubilityTableFormula(_formulaFactory.CreateTableFormula(), refPh.Dimension, refSolubility.Dimension);
compoundForCalculation.Parameter(CoreConstants.Parameters.REFERENCE_PH).Value = refPh.Value;
compoundForCalculation.Parameter(CoreConstants.Parameters.SOLUBILITY_GAIN_PER_CHARGE).Value = gainPerCharge.Value;
double solFactorRefpH = compoundForCalculation.Parameter(CoreConstants.Parameters.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)
{
compoundForCalculation.Parameter(CoreConstants.Parameters.REFERENCE_PH).Value = pH;
double solFactorAtpH = compoundForCalculation.Parameter(CoreConstants.Parameters.SOLUBILITY_P_KA__P_H_FACTOR).Value;
formula.AddPoint(pH, refSolubilityValue * solFactorRefpH / solFactorAtpH);
}
return(formula);
}
public LipophilictyAlternativeDTO MapFrom(ParameterAlternative parameterAlternative)
{
var lipophilictyAlternativeDTO = new LipophilictyAlternativeDTO(parameterAlternative);
var lipophilicity = parameterAlternative.Parameter(CoreConstants.Parameter.Lipophilicity);
lipophilictyAlternativeDTO.LipophilictyParameter = _parameterDTOMapper.MapFrom(lipophilicity, lipophilictyAlternativeDTO, dto => dto.Lipophilicty, dto => dto.LipophilictyParameter);
return(lipophilictyAlternativeDTO);
}
public SolubilityAlternativeDTO MapFrom(ParameterAlternative parameterAlternative)
{
var solubilityAtRefPh = parameterAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_AT_REFERENCE_PH);
var solubilityTable = parameterAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_TABLE);
var solubilityParameter = solubilityTable.Formula.IsTable() ? solubilityTable : solubilityAtRefPh;
var solubilityAlternativeDTO = new SolubilityAlternativeDTO(parameterAlternative, solubilityParameter.ValueOrigin);
solubilityAlternativeDTO.SolubilityParameter = _parameterDTOMapper.MapFrom(solubilityParameter, solubilityAlternativeDTO, dto => dto.Solubility, dto => dto.SolubilityParameter);
var refPh = parameterAlternative.Parameter(CoreConstants.Parameters.REFERENCE_PH);
solubilityAlternativeDTO.RefpHParameter = _parameterDTOMapper.MapFrom(refPh, solubilityAlternativeDTO, dto => dto.RefpH, dto => dto.RefpHParameter);
var gainPerCharge = parameterAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_GAIN_PER_CHARGE);
solubilityAlternativeDTO.GainPerChargeParameter = _parameterDTOMapper.MapFrom(gainPerCharge, solubilityAlternativeDTO, dto => dto.GainPerCharge, dto => dto.GainPerChargeParameter);
return(solubilityAlternativeDTO);
}
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);
}
public void should_have_set_the_compound_specific_parameter_using_the_defined_value_if_available()
{
_result.Parameter(CoreConstants.Parameters.FRACTION_UNBOUND_EXPERIMENT).Value.ShouldBeEqualTo(_fuAlternative.Parameter(CoreConstants.Parameters.FRACTION_UNBOUND_PLASMA_REFERENCE_VALUE).Value);
}
public void should_have_set_the_compound_specific_parameter_using_the_defined_value_if_available()
{
_result.Parameter(CoreConstants.Parameter.FRATION_UNBOUND_EXPERIMENT).Value.ShouldBeEqualTo(_fuAlternative.Parameter(CoreConstants.Parameter.FractionUnbound).Value);
}
public void should_have_added_a_clone_of_the_template_paraemter_for_the_given_group_to_the_alternative()
{
_newAlternative.Parameter(CoreConstants.Parameters.SOLUBILITY_TABLE).ShouldBeEqualTo(_solubilityTable);
}
protected override void Because()
{
_result = sut.CreateAlternativeFor(_compoundParameterGroup);
_alternativeParameter = _result.Parameter("toto");
}