632 import concentration based sbml files #633
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| molInfo.SetDimension(newDim); | ||
| msv.Formula = _context.Create<ExplicitFormula>($"{msv.Name}_0").WithName($"{msv.Name}_0").WithDimension(amountDimension).WithFormulaString($"{baseValue.value} * {Constants.VOLUME_ALIAS}"); | ||
| msv.Formula.AddObjectPath( | ||
| ObjectPathFactory.CreateFormulaUsablePathFrom(ObjectPath.PARENT_CONTAINER, Constants.Parameters.VOLUME) |
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@msevestre Check the change in the call. This is why the Volume was not found before. It should not be one single string but the list of all individual paths
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Also, it would be very nice to use the code base for concentration based reactions, but the way the importer is written it is not trivial to me. I would propose to keep it in mind for the future but just use this solution for now.
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sounds good. What about the reaction rate? Aren;t they expecting concentration?
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@msevestre I think this is related to the second PR, right?
| @@ -191,6 +196,7 @@ private void SetMoleculeStartValues(Model model) | |||
| if (molInfo.GetContainer().Any(x => x.Name == msv.ContainerPath.LastOrDefault())) | |||
| { | |||
| msv.IsPresent = true; | |||
| msv.NegativeValuesAllowed = true; | |||
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for 99.9% of MSV the reasonable setting is NegativeValuesAllowed = false
If the msv entry is one of the remaining 0.1% or if there are some numerical issues - it still can be set to true by user.
@PavelBal
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@Yuri05 is right, it can be manually set.
…lues" This reverts commit d6830f4.
| molInfo.SetDimension(newDim); | ||
| msv.Formula = _context.Create<ExplicitFormula>($"{msv.Name}_0").WithName($"{msv.Name}_0").WithDimension(amountDimension).WithFormulaString($"{baseValue.value} * {Constants.VOLUME_ALIAS}"); | ||
| msv.Formula.AddObjectPath( | ||
| ObjectPathFactory.CreateFormulaUsablePathFrom(ObjectPath.PARENT_CONTAINER, Constants.Parameters.VOLUME) |
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sounds good. What about the reaction rate? Aren;t they expecting concentration?
| { | ||
| var gkReaction = _moBiProject.ReactionBlockCollection.First().First(); | ||
| var glucosePath = gkReaction.Formula.ObjectPaths.ElementAt(1); | ||
| glucosePath.Last().ShouldBeEqualTo("Concentration"); |
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Let's use the constant instead of a magic screen
| } | ||
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| [Observation] | ||
| public void ShouldParseUserDefinedFunctions() |
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should_parse_user_defined_functions
Fixes #632 (Import from SBML File with concentration based reactions)