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Open-Systems-Pharmacology / PK-Sim

PK-Sim® is a comprehensive software tool for whole-body physiologically based pharmacokinetic modeling
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MoleculeType is not set for most TwoPore Molecules #243

Open msevestre opened 7 years ago

msevestre commented 7 years ago

see project defined here (MoBi project but this is clear then) https://github.com/Open-Systems-Pharmacology/Forum/issues/46

FcRn_XXX Molecules as well as LingandEndo and LingandEndo_Complex do not have the right MoleculeType

msevestre commented 7 years ago

@Yuri05 what should they be?

StephanSchaller commented 7 years ago

Proteins

msevestre commented 6 years ago

@Yuri05 ping :)

StephanSchaller commented 6 years ago

or "Protein complex" :-)

msevestre commented 6 years ago

@StephanSchaller I am talking here about the internal QuantityType which is a predefined property of a molecule. Depending on this quantity type, some action may or may not occur and it should be set accordingly.

As you can see, we already have Protein and Complex. Protein is a combine type so this should DEFINITELY not be used. Complex maybe but this seems wrong.

Yuri05 commented 1 year ago

I tried to change the molecule type for FcRn etc. to "OtherProteins" in the database, but somehow it did not work (FcRn etc. are still shown without Icon'; when exported to MoBi their Molecule Type is still set to empty. In PK-Sim in Debug mode I can see however that the molecule type is properly set:

?All().ToList()[1]
{PKSim.Infrastructure.ORM.FlatObjects.FlatMolecule}
    CalculationMethod: "CompoundCommon"
    Id: "FcRn"
    IsFloating: true
    MoleculeType: OtherProtein
    Rate: "Zero_Rate"

Also switching the Molecule type from Undefinedto Other Protein would change the generation of the molecule - which I'm not sure if it would be correct then - probably not. So I will rollback the change for now. https://github.com/Open-Systems-Pharmacology/PK-Sim/blob/0b33736c8b7efe83c2faf743fd12a54587d3e4bb/src/PKSim.Infrastructure/Services/MoleculeBuilderFactory.cs#L73-L81

PavelBal commented 1 year ago

I would like to re-design the whole FcRn model by using state variable parameters instead of molecules (which are only present in some containers) to make it easier to extend. I started to do so but didn't have the time to finalize