private Model.CompoundProcess notSelectedProcessFrom(CompoundProcessSelection snapshotCompoundProcessSelection, ISimulationSubject simulationSubject)
{
//Partial process
var moleculeName = snapshotCompoundProcessSelection.MoleculeName;
var systemicProcessType = snapshotCompoundProcessSelection.SystemicProcessType;
//this should be a specific process
if (!string.IsNullOrEmpty(systemicProcessType))
{
return new NotSelectedSystemicProcess {
SystemicProcessType = SystemicProcessTypes.ById(systemicProcessType)
}
}
;
if (string.IsNullOrEmpty(moleculeName))
{
return(null);
}
var molecule = simulationSubject.MoleculeByName(moleculeName);
if (molecule == null)
{
return(null);
}
switch (molecule)
{
case IndividualTransporter _:
return(new TransportPartialProcess {
MoleculeName = moleculeName
});
case IndividualEnzyme _:
return(new EnzymaticProcess {
MoleculeName = moleculeName
});
case IndividualOtherProtein _:
return(new SpecificBindingPartialProcess {
MoleculeName = moleculeName
});
}
return(null);
}
public ModelCompound MapFrom(BatchCompound batchCompound)
{
var compound = _compoundFactory.Create();
compound.Name = batchCompound.Name;
setValue(compound, CoreConstants.Groups.COMPOUND_LIPOPHILICITY,
CoreConstants.Parameter.LIPOPHILICITY, batchCompound.Lipophilicity);
setValue(compound, CoreConstants.Groups.COMPOUND_FRACTION_UNBOUND,
CoreConstants.Parameter.FractionUnbound, batchCompound.FractionUnbound);
setValue(compound, Constants.Parameters.MOL_WEIGHT, batchCompound.MolWeight);
setValue(compound, CoreConstants.Parameter.CL, batchCompound.Cl);
setValue(compound, CoreConstants.Parameter.F, batchCompound.F);
setValue(compound, CoreConstants.Parameter.BR, batchCompound.Br);
setValue(compound, CoreConstants.Parameter.I, batchCompound.I);
setValue(compound, CoreConstants.Parameter.IS_SMALL_MOLECULE, batchCompound.IsSmallMolecule ? 1 : 0);
setValue(compound, CoreConstants.Groups.COMPOUND_SOLUBILITY,
CoreConstants.Parameter.SolubilityAtRefpH, batchCompound.SolubilityAtRefpH);
setValue(compound, CoreConstants.Groups.COMPOUND_SOLUBILITY,
CoreConstants.Parameter.RefpH, batchCompound.RefpH);
for (int i = 0; i < batchCompound.PkaTypes.Count; i++)
{
setPka(compound, batchCompound.PkaTypes[i], i);
}
foreach (var batchSystemicProcess in batchCompound.SystemicProcesses)
{
var systemicProcess = retrieveProcessFrom <Model.SystemicProcess>(batchSystemicProcess);
if (systemicProcess == null)
{
continue;
}
systemicProcess.SystemicProcessType = SystemicProcessTypes.ById(batchSystemicProcess.SystemicProcessType);
systemicProcess.RefreshName();
compound.AddProcess(systemicProcess);
}
foreach (var batchPartialProcess in batchCompound.PartialProcesses)
{
var partialProcess = retrieveProcessFrom <Model.PartialProcess>(batchPartialProcess);
if (partialProcess == null)
{
continue;
}
partialProcess.MoleculeName = batchPartialProcess.MoleculeName;
partialProcess.RefreshName();
compound.AddProcess(partialProcess);
}
//Update default with available CM in configuration
foreach (var calculationMethodName in batchCompound.CalculationMethods)
{
var calculationMethod = _calculationMethodRepository.FindByName(calculationMethodName);
if (calculationMethod == null)
{
_batchLogger.AddWarning($"Calculation method '{calculationMethodName}' not found");
continue;
}
var category = _calculationMethodCategoryRepository.FindByName(calculationMethod.Category);
if (category == null)
{
_batchLogger.AddWarning($"Could not find compound category '{calculationMethod.Category}' for calculation method '{calculationMethodName}.");
continue;
}
//this is a compound calculationmethod. Swap them out
var existingCalculationMethod = compound.CalculationMethodFor(category);
compound.RemoveCalculationMethod(existingCalculationMethod);
compound.AddCalculationMethod(calculationMethod);
_batchLogger.AddDebug($"Using calculation method '{calculationMethod.Name}' instead of '{existingCalculationMethod.Name}' for category '{calculationMethod.Category}'");
}
return(compound);
}
public override object ConvertFrom(string attributeValue, SerializationContext context)
{
return(SystemicProcessTypes.ById(attributeValue));
}