/// <summary>
/// Creates a MoBi ReactionPartner by a given SBML Species Reference
/// </summary>
private IReactionPartnerBuilder CreateReactionPartner(SpeciesReference speciesReference, Model model)
{
var molecule = _sbmlInformation.GetMoleculeBySBMLId(speciesReference.getSpecies());
if (molecule == null)
{
return(null);
}
IReactionPartnerBuilder productBuilder = new ReactionPartnerBuilder
{
MoleculeName = molecule.Name,
};
if (speciesReference.isSetStoichiometryMath())
{
CreateStoichiometryErrorMsg(speciesReference.getSpecies());
}
productBuilder.StoichiometricCoefficient = speciesReference.isSetStoichiometry() ? speciesReference.getStoichiometry() : SBMLConstants.SBML_STOICHIOMETRY_DEFAULT;
var species = GetSpeciesById(speciesReference.getSpecies(), model);
if (species == null)
{
return(productBuilder);
}
if (species.getConstant() && species.getBoundaryCondition() == false)
{
productBuilder.StoichiometricCoefficient = 0;
}
return(productBuilder);
}
private void addReactionPartnerTo(PKSimReaction reaction, FlatReactionPartner flatReactionPartner)
{
if (flatReactionPartner.Direction.Equals(CoreConstants.ORM.PROCESS_MOLECULE_DIRECTION_MODIFIER))
{
//---- not Educt/Product, just a modifier
reaction.AddModifier(flatReactionPartner.Molecule);
return;
}
//---- from now on, must be educt/product
var reactionPartner = new ReactionPartnerBuilder()
{
MoleculeName = flatReactionPartner.Molecule,
StoichiometricCoefficient = flatReactionPartner.StoichCoeff
};
if (flatReactionPartner.Direction.Equals(CoreConstants.ORM.PROCESS_MOLECULE_DIRECTION_IN))
{
reaction.AddEduct(reactionPartner);
return;
}
if (flatReactionPartner.Direction.Equals(CoreConstants.ORM.PROCESS_MOLECULE_DIRECTION_OUT))
{
reaction.AddProduct(reactionPartner);
return;
}
//invalid direction (should never happen)
throw new ArgumentOutOfRangeException(flatReactionPartner.Direction);
}
protected override void Context()
{
_simulation = new ModelCoreSimulation();
var root = new Container();
root.Add(new EventGroup());
_simulation.Model = new Model();
_simulation.Model.Root = root;
_simulation.BuildConfiguration = new BuildConfiguration();
var reactionBuildingBlock = new ReactionBuildingBlock();
var reactionAtoB = new ReactionBuilder();
var reactionBtoA = new ReactionBuilder();
var partnerA = new ReactionPartnerBuilder("A", 0);
var partnerB = new ReactionPartnerBuilder("B", 0);
//Making both reactions dependent on each other
reactionAtoB.AddProduct(partnerA);
reactionBtoA.AddProduct(partnerB);
reactionAtoB.AddEduct(partnerB);
reactionBtoA.AddEduct(partnerA);
reactionBuildingBlock.Add(reactionAtoB);
reactionBuildingBlock.Add(reactionBtoA);
_simulation.BuildConfiguration.Reactions = reactionBuildingBlock;
}
public void TestSerialization()
{
var x1 = new ReactionPartnerBuilder("H2O", 3.1);
var x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualReactionPartnerBuilder(x1, x2);
}
/// <summary>
/// Creates a reaction product with the default stoichiometry.
/// </summary>
private static IReactionPartnerBuilder CreateProduct(string molculeName)
{
IReactionPartnerBuilder productBuilder = new ReactionPartnerBuilder
{
MoleculeName = molculeName
};
productBuilder.StoichiometricCoefficient = SBMLConstants.SBML_STOICHIOMETRY_DEFAULT;
return(productBuilder);
}
protected override void Context()
{
base.Context();
_reactionBuilder = new ReactionBuilder();
var reactionPartnerBuilder = new ReactionPartnerBuilder("A", 1);
_reactionBuilder.AddProduct(reactionPartnerBuilder);
_dto = new ReactionPartnerBuilderDTO(reactionPartnerBuilder);
A.CallTo(() => _reactionProductsPresenter.Subject).Returns(_reactionBuilder);
}
protected override void Context()
{
base.Context();
_reactionPartnerBuilder = new ReactionPartnerBuilder("moleculeName", 2.0);
_reactionPartnerDTO = new ReactionPartnerBuilderDTO(_reactionPartnerBuilder);
_reactionBuilderDTO.Educts.Add(_reactionPartnerDTO);
_reactionBuilderDTO.ReactionBuilder.AddEduct(_reactionPartnerBuilder);
_reactionBuildingBlock.DiagramModel = A.Fake <IDiagramModel>();
A.CallTo(() => _interactionTaskForReactionBuilder.SelectMoleculeNames(_reactionBuildingBlock, A <IEnumerable <string> > ._, A <string> ._, AppConstants.Captions.Educts)).Returns(new List <string> {
"moleculeName"
});
sut.Edit(_reactionBuilderDTO, _reactionBuildingBlock);
}
protected override void Context()
{
_oldMoleculeName = "A";
_newMoleculeName = "B";
_reaction = new ReactionBuilder().WithId("R");
_reactionPartner = new ReactionPartnerBuilder(_oldMoleculeName, 3);
_buildingBlock = A.Fake <IMoBiReactionBuildingBlock>().WithId("BB");
_context = A.Fake <IMoBiContext>();
A.CallTo(() => _context.Get <IReactionBuilder>(_reaction.Id)).Returns(_reaction);
A.CallTo(() => _context.Get <IMoBiReactionBuildingBlock>(_buildingBlock.Id)).Returns(_buildingBlock);
AddPartnerToReaction();
_diagramManager = A.Fake <IMoBiReactionDiagramManager>();
A.CallTo(() => _buildingBlock.DiagramManager).Returns(_diagramManager);
sut = new EditReactionPartnerMoleculeNameCommand(_newMoleculeName, _reaction, _reactionPartner, _buildingBlock);
}
