private void addSystemicProcesses(Model.Compound compound, ProcessSelectionGroup processSelectionGroup, SystemicProcessType systemicProcessType)
{
//add all systemic processes
compound.AllSystemicProcessesOfType(systemicProcessType).Each(systemicProcess =>
{
var processSelection = new SystemicProcessSelection {
ProcessName = systemicProcess.Name, ProcessType = systemicProcess.SystemicProcessType
};
processSelectionGroup.AddSystemicProcessSelection(processSelection);
});
}
private CompoundGroupSelection[] alternativeSelectionsFrom(Model.Compound compound, ModelCompoundProperties modelCompoundProperties)
{
var alternativesSelections = new List <CompoundGroupSelection>();
modelCompoundProperties.CompoundGroupSelections.Each(x =>
{
var compoundProperties = compound.ParameterAlternativeGroup(x.GroupName);
if (compoundProperties.AllAlternatives.Count() > 1)
{
alternativesSelections.Add(x);
}
});
return(!alternativesSelections.Any() ? null : alternativesSelections.ToArray());
}
private async Task <CompoundProcessesSelection> modelProcessSelectionFrom(CompoundProcessSelection[] snapshotProcesses, Model.Compound compound, ISimulationSubject simulationSubject, SnapshotContext snapshotContext)
{
var compoundProcessesSelection = new CompoundProcessesSelection();
if (snapshotProcesses == null)
{
return(compoundProcessesSelection);
}
foreach (var snapshotProcess in snapshotProcesses)
{
var process = compound.ProcessByName(snapshotProcess.Name) ?? notSelectedProcessFrom(snapshotProcess, simulationSubject);
if (process == null)
{
//No process found and a name was specified. This is a snapshot that is corrupted
if (!string.IsNullOrEmpty(snapshotProcess.Name))
{
_logger.AddWarning(PKSimConstants.Error.ProcessNotFoundInCompound(snapshotProcess.Name, compound.Name));
}
continue;
}
await addProcessToProcessSelection(compoundProcessesSelection, snapshotProcess, process, snapshotContext);
}
return(compoundProcessesSelection);
}
private async Task <CompoundProcessesSelection> modelProcessSelectionFrom(CompoundProcessSelection[] snapshotProcesses, Model.Compound compound)
{
var compoundProcessesSelection = new CompoundProcessesSelection();
if (snapshotProcesses == null)
{
return(compoundProcessesSelection);
}
foreach (var snapshotProcess in snapshotProcesses)
{
var process = compound.ProcessByName(snapshotProcess.Name);
if (process == null)
{
_logger.AddWarning(PKSimConstants.Error.ProcessNotFoundInCompound(snapshotProcess.Name, compound.Name));
}
else
{
await addProcessToProcessSelection(compoundProcessesSelection, snapshotProcess, process);
}
}
return(compoundProcessesSelection);
}
private void addPartialProcesses <TPartialProcess, TIndividualMolecule, TProcessSelection>(Model.Compound compound, Model.Individual individual, ProcessSelectionGroup processSelectionGroup)
where TPartialProcess : Model.PartialProcess
where TIndividualMolecule : IndividualMolecule
where TProcessSelection : ProcessSelection, new()
{
//default mapping with processes: Mapping done only by name
foreach (var process in compound.AllProcesses <TPartialProcess>())
{
var molecule = individual.MoleculeByName <TIndividualMolecule>(process.MoleculeName);
//enzyme not found in individual
if (molecule == null)
{
_batchLogger.AddDebug($"Molecule '{process.MoleculeName}' not found in individual but is defined in compound for process '{process.Name}'");
continue;
}
_batchLogger.AddDebug($"Adding process {process.Name} for molecule {molecule.Name}");
processSelectionGroup.AddPartialProcessSelection(new TProcessSelection {
ProcessName = process.Name, MoleculeName = molecule.Name, CompoundName = compound.Name
});
}
}
