SpringSaLaD: auto-generated _tot observables land in the wrong structure, and there is no way to move one

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Valutazione

Difficoltà
3/5
Tempo stimato
Mezza giornata
Idoneità per principianti
72/100
Tipo di issue
Bug
Chiarezza
Specificata chiaramente
Stato di attività
Attiva
Stack tecnologico
java
Ambito
desktop

Direzione di ricerca

Start at Model.createObservable in vcell-core/src/main/java/bit/vcell/model/Model.java:1524-1550 (actual path vcell-core/src/main/java/bit/vcell/... per payload: vcell-core/src/main/java/bit/vcell/model/Model.java) and see how the getStructure(0) fallback interacts with a molecule's anchor restriction. Then inspect ObservableTableModel:195 for the Structure column and addObservable's empty SpeciesPattern seed. Done looks like: creating an anchored molecule yields an observable in a valid structure with no Problems-tab warning, verified by the three-compartment SpringSaLaD reproduction.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Found while writing a SpringSaLaD tutorial script. In a three-compartment SpringSaLaD
model, every observable VCell creates for you lands in Extracellular, and for an
anchored molecule that is a standing warning with no remedy but deletion.

What happens

Creating a molecule creates an observable counting it. Model.createObservable
(vcell-core/src/main/java/cbit/vcell/model/Model.java:1524-1550) falls back to
getStructure(0) when no structure is given, and in a SpringSaLaD model structure 0 is
Extracellular.

For a molecule anchored to the membrane, that is immediately wrong, and the Problems tab
says so:

Molecule RK cannot be present in the structure due to anchoring.

The Structure column is not editable — ObservableTableModel:195 returns false for it
unconditionally — so the observable cannot be moved to where it belongs.

And the replacement route leaves its own complaint

The obvious workaround is to delete it and create a new one through
New > In Membrane Membrane, which does ask for a compartment. That produces an observable
in the right structure with the right pattern, and a different warning:

Molecule of Species Pattern is empty.

addObservable(o) seeds the new observable with o.addSpeciesPattern(new SpeciesPattern()),
and setting the BioNetGen definition afterwards does not consume that empty pattern. There
is no table-reachable way to remove it.

So neither path reaches a clean model, and the only way to have no warnings is to have no
observable for the anchored molecule at all.

Reproduction

  1. Three structures named Extracellular / Membrane / Intracellular.
  2. A molecule RK(B~State0~State1,Anchor~Anchor,K~Off~On), anchored to Membrane via
    Object Properties > "Only these:" > Membrane.
  3. A seed species for it, created In Membrane Membrane.
  4. Look at Observables, and at the Problems tab.

Suggested fixes

  • The auto path could use the molecule's anchor. When a molecule is restricted to one
    structure, that structure is the only sensible home for an observable counting it.
  • Failing that, make the Structure column editable, restricted to the structures the
    molecule is allowed in.
  • Separately, the empty seed species pattern should be consumed when a definition is set,
    or not created until there is something to put in it.

Note

Nothing is actually lost for a SpringSaLaD run: LangevinLngvWriter does not read
observables at all, and SpringSaLaD results come from the solver's own molecule, state,
bond, site and cluster counters. The cost is a model that cannot be made warning-free,
which matters most to a new user who does not yet know which warnings to ignore.

Lingua principale
Java
Stelle
140
Fork
35
Merge medio
22h 6m
PR unite (30g)
14

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