public IndividualTransporter CreateFor(ISimulationSubject simulationSubject, string moleculeName, TransportType transporterType)
{
var transporter = CreateMolecule(moleculeName);
if (HasAgeParameter(simulationSubject))
{
AddOntogenyParameterTo(transporter);
}
//default transporter type
transporter.TransportType = transporterType;
//default transport direction
addGlobalExpression(transporter, BLOOD_CELLS, DefaultBloodCellsDirectionFor(transporterType), RelExpParam(REL_EXP_BLOOD_CELLS));
//Special direction for vascular endothelium that is independent from the default direction choice
addGlobalExpression(transporter, VASCULAR_ENDOTHELIUM, DefaultVascularEndotheliumDirectionFor(transporterType),
RelExpParam(REL_EXP_VASCULAR_ENDOTHELIUM));
addVascularSystemInitialConcentration(simulationSubject, transporter);
addTissueOrgansExpression(simulationSubject, transporter);
addMucosaExpression(simulationSubject, transporter);
simulationSubject.AddMolecule(transporter);
_individualPathWithRootExpander.AddRootToPathIn(simulationSubject, moleculeName);
return(transporter);
}
private void finalizeIndividual(Individual individual)
{
if (individual == null)
{
return;
}
_neighborhoodFinalizer.SetNeighborsIn(individual);
_individualPathWithRootExpander.AddRootToPathIn(individual);
_keywordReplacerTask.ReplaceIn(individual);
_referencesResolver.ResolveReferencesIn(individual);
}
public override IndividualMolecule AddMoleculeTo(ISimulationSubject simulationSubject, string moleculeName)
{
var molecule = CreateMolecule(moleculeName);
if (HasAgeParameter(simulationSubject))
{
AddOntogenyParameterTo(molecule);
}
//default localization
molecule.Localization = Localization.Intracellular;
AddGlobalExpression(molecule,
RelExpParam(REL_EXP_BLOOD_CELLS),
FractionParam(FRACTION_EXPRESSED_BLOOD_CELLS, CoreConstants.Rate.ONE_RATE),
FractionParam(FRACTION_EXPRESSED_BLOOD_CELLS_MEMBRANE, CoreConstants.Rate.PARAM_F_EXP_BC_MEMBRANE)
);
AddGlobalExpression(molecule, RelExpParam(REL_EXP_PLASMA));
AddGlobalExpression(molecule,
RelExpParam(REL_EXP_VASCULAR_ENDOTHELIUM),
FractionParam(FRACTION_EXPRESSED_VASC_ENDO_ENDOSOME, CoreConstants.Rate.ONE_RATE),
FractionParam(FRACTION_EXPRESSED_VASC_ENDO_PLASMA_SIDE, CoreConstants.Rate.ZERO_RATE),
FractionParam(FRACTION_EXPRESSED_VASC_ENDO_TISSUE_SIDE, CoreConstants.Rate.PARAM_F_EXP_VASC_TISSUE_SIDE)
);
addVascularSystemInitialConcentration(simulationSubject, moleculeName);
AddTissueOrgansExpression(simulationSubject, moleculeName);
AddLumenExpression(simulationSubject, moleculeName);
AddMucosaExpression(simulationSubject, moleculeName);
simulationSubject.AddMolecule(molecule);
_individualPathWithRootExpander.AddRootToPathIn(simulationSubject, moleculeName);
return(molecule);
}