public IParameter CreateFor(ParameterRateMetaData parameterRateDefinition, IFormulaCache formulaCache)
{
var param = _objectBaseFactory.CreateParameter();
param.Formula = _formulaFactory.RateFor(parameterRateDefinition, formulaCache);
if (!string.IsNullOrEmpty(parameterRateDefinition.RHSRate))
{
param.RHSFormula = _formulaFactory.RHSRateFor(parameterRateDefinition, formulaCache);
}
setParameterProperties(param, parameterRateDefinition);
updateDefaultValueFor(param);
return(param);
}
private void setStartFormulasForStaticMolecules(IMoleculeStartValuesBuildingBlock defaultStartValues, Simulation simulation, IEnumerable <Compound> compounds)
{
var modelName = simulation.ModelConfiguration.ModelName;
//get the names of molecules that are static (e.g. not enzymes, metabolites, etc.)
// (e.g. FcRn in 2pores-model)
var staticMoleculeNames = _modelContainerMoleculeRepository.MoleculeNamesIncludingDrug(modelName);
var compoundNames = compounds.AllNames().ToList();
foreach (var moleculeStartValue in defaultStartValues)
{
var dbMoleculeName = getDbMoleculeName(moleculeStartValue.MoleculeName, compoundNames);
if (staticMoleculeNames.Contains(dbMoleculeName))
{
moleculeStartValue.IsPresent = _modelContainerMoleculeRepository.IsPresent(modelName, moleculeStartValue.ContainerPath, dbMoleculeName);
moleculeStartValue.NegativeValuesAllowed = _modelContainerMoleculeRepository.NegativeValuesAllowed(modelName, moleculeStartValue.ContainerPath, dbMoleculeName);
}
else
{
moleculeStartValue.IsPresent = false;
moleculeStartValue.NegativeValuesAllowed = false;
}
var moleculeDbPath = moleculeStartValue.ContainerPath.Clone <IObjectPath>();
moleculeDbPath.Add(dbMoleculeName);
var rateKey = _moleculeStartFormulaRepository.RateKeyFor(moleculeDbPath, simulation.ModelProperties);
if (rateKey == null)
{
continue; //no start formula available
}
//set molecule start formula
moleculeStartValue.Formula = _formulaFactory.RateFor(rateKey, defaultStartValues.FormulaCache);
}
}
