private string membraneContainerDisplayName(MembraneLocation membraneLocation, TransporterExpressionContainerDTO containerDTO)
{
return($"{containerDTO.ContainerPathDTO.DisplayName} ({membraneLocation})");
}
public void MembraneLocationChanged(MembraneLocation membraneLocation)
{
AddCommand(_moleculeExpressionTask.SetMembraneLocationFor(_protein, membraneLocation));
}
public void SetMembraneLocation(TransporterExpressionContainerDTO transporterExpressionContainerDTO, MembraneLocation membraneLocation)
{
AddCommand(_moleculeExpressionTask.SetMembraneLocationFor(transporterContainerFrom(transporterExpressionContainerDTO), _transporter.TransportType, membraneLocation));
}
public ICommand SetMembraneLocationFor(TransporterExpressionContainer transporterContainer, TransportType transportType, MembraneLocation membraneLocation)
{
return(new SetMembraneTypeCommand(transporterContainer, transportType, membraneLocation, _executionContext).Run(_executionContext));
}
public ICommand SetMembraneLocationFor(IndividualProtein protein, MembraneLocation membraneLocation)
{
return(new SetProteinMembraneLocationCommand(protein, membraneLocation, _executionContext).Run(_executionContext));
}
protected override void PerformExecuteWith(IExecutionContext context)
{
_oldMembraneLocation = _protein.MembraneLocation;
_protein.MembraneLocation = _newMembraneLocation;
Description = PKSimConstants.Command.SetProteinMembraneLocationDescription(_oldMembraneLocation.ToString(), _newMembraneLocation.ToString());
}
public void UpdateTransporterFromTemplate(ITransporterExpressionContainer transporterContainer, string species, MembraneLocation membraneLocation, TransportType transportType)
{
//we need to retrieve the process name for the given MembraneTupe/Process Type combo
var templateToUse = _transporterContainerTemplateRepository.TransportersFor(species, transporterContainer.Name)
.Where(x => x.MembraneLocation == membraneLocation)
.FirstOrDefault(x => x.TransportType == transportType);
//That should never happen, otherwise we would have a transporter container with an unknown process
if (templateToUse == null)
{
throw new PKSimException(PKSimConstants.Error.CouldNotFindTransporterFor(transporterContainer.Name, membraneLocation.ToString(), transportType.ToString()));
}
transporterContainer.UpdatePropertiesFrom(templateToUse);
}
private string membraneContainerDisplayName(MembraneLocation membraneLocation, TransporterExpressionContainerDTO containerDTO)
{
return(string.Format("{0} ({1})", containerDTO.ContainerPathDTO.DisplayName, membraneLocation));
}
public SetProteinMembraneLocationCommand(PKSim.Core.Model.IndividualProtein protein, MembraneLocation membraneLocation, IExecutionContext context)
{
_protein = protein;
BuildingBlockId = context.BuildingBlockIdContaining(protein);
_newMembraneLocation = membraneLocation;
ObjectType = PKSimConstants.ObjectTypes.Protein;
CommandType = PKSimConstants.Command.CommandTypeEdit;
_proteinId = _protein.Id;
context.UpdateBuildinBlockPropertiesInCommand(this, context.BuildingBlockContaining(_protein));
}
public SetMembraneTypeCommand(TransporterExpressionContainer transporterContainer, TransportType transportType, MembraneLocation newMembraneLocation, IExecutionContext context)
{
_transporterContainer = transporterContainer;
_transportType = transportType;
_transporterContainerId = _transporterContainer.Id;
_newMembraneLocation = newMembraneLocation;
_individual = context.BuildingBlockContaining(_transporterContainer).DowncastTo <Individual>();
BuildingBlockId = _individual.Id;
_oldMembraneLocation = _transporterContainer.MembraneLocation;
ObjectType = PKSimConstants.ObjectTypes.Transporter;
CommandType = PKSimConstants.Command.CommandTypeEdit;
context.UpdateBuildinBlockPropertiesInCommand(this, _individual);
}
public SetTransportTypeCommand(TransporterExpressionContainer transporterContainer, TransportType oldTransportType, TransportType newTransportType, MembraneLocation membraneLocationToUse, IExecutionContext context)
{
_transporterContainer = transporterContainer;
_membraneLocationToUse = membraneLocationToUse;
_transporterContainerId = _transporterContainer.Id;
_individual = context.BuildingBlockContaining(transporterContainer).DowncastTo <Individual>();
BuildingBlockId = _individual.Id;
_newTransportType = newTransportType;
_oldTransportType = oldTransportType;
ObjectType = PKSimConstants.ObjectTypes.Transporter;
CommandType = PKSimConstants.Command.CommandTypeEdit;
context.UpdateBuildinBlockPropertiesInCommand(this, _individual);
Visible = false;
}
private static void validateTransporterMembrane(IndividualTransporter transporter, MembraneLocation membraneLocation)
{
CoreConstants.Compartment.LiverZones.Each(z => transporter.AllExpressionsContainers().FindByName(z).MembraneLocation.ShouldBeEqualTo(membraneLocation));
}
public static Localization ConvertToLocalization(TissueLocation tissueLocation, MembraneLocation membraneLocation,
IntracellularVascularEndoLocation vascularEndoLocation)
{
switch (tissueLocation)
{
case TissueLocation.Interstitial:
return(Localization.Interstitial | Localization.BloodCellsIntracellular | Localization.VascMembraneTissueSide);
case TissueLocation.Intracellular:
var vacEndoLocalization = vascularEndoLocation == IntracellularVascularEndoLocation.Endosomal
? Localization.VascEndosome
: Localization.VascMembraneTissueSide;
return(Localization.Intracellular | Localization.BloodCellsIntracellular | vacEndoLocalization);
case TissueLocation.ExtracellularMembrane:
var membLocation = membraneLocation == MembraneLocation.Apical
? Localization.VascMembranePlasmaSide
: Localization.VascMembraneTissueSide;
return(Localization.Interstitial | Localization.BloodCellsMembrane | membLocation);
default:
throw new ArgumentOutOfRangeException(nameof(tissueLocation), tissueLocation, null);
}
}
public static void ConvertMembraneLocationToParameterFraction(IReadOnlyList <TransporterExpressionContainer> transporterExpressionContainers, MembraneLocation membraneLocation)
{
var firstContainer = transporterExpressionContainers[0];
if (firstContainer.LogicalContainer.IsBrain())
{
//Is there by construction
var plasma = transporterExpressionContainers.First(x => x.CompartmentName == PLASMA);
var fractionBBB = plasma.Parameter(FRACTION_EXPRESSED_AT_BLOOD_BRAIN_BARRIER);
switch (membraneLocation)
{
//we need to set the value of f_bbb to zero
case MembraneLocation.Tissue:
fractionBBB.Value = 0;
return;
//we need to set the value of f_bbb to 1
case MembraneLocation.BloodBrainBarrier:
fractionBBB.Value = 1;
return;
}
}
if (firstContainer.LogicalContainer.IsOrganWithLumen())
{
//Is there by construction
var intracellular = transporterExpressionContainers.First(x => x.CompartmentName == INTRACELLULAR);
var fractionExpressedApical = intracellular.Parameter(FRACTION_EXPRESSED_APICAL);
switch (membraneLocation)
{
//we need to set the value of f_expressed_apical to zero
case MembraneLocation.Basolateral:
fractionExpressedApical.Value = 0;
return;
//we need to set the value of f_bbb to 1
case MembraneLocation.Apical:
fractionExpressedApical.Value = 1;
return;
}
}
//this should never happen
}
