public IMoleculeBuilder GetMoleculeBySBMLId(string sbmlSpeciesId)
{
var moleculeInformation = MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Exists(s => s == sbmlSpeciesId));
if (moleculeInformation == null)
{
return(null);
}
var molecule = moleculeInformation.GetMoleculeBuilder();
return(molecule);
}
protected override void Context()
{
base.Context();
_sbmlModel = new Model(3, 1);
_sbmlInformation = new SBMLInformation();
//one compartment reaction
_reaction = _sbmlModel.createReaction();
_reaction.setId("r1");
//reaction partner
var s1 = _sbmlModel.createSpecies();
s1.setId("s1");
s1.setCompartment("default");
var s2 = _sbmlModel.createSpecies();
s2.setId("s2");
s2.setCompartment("default");
var m = new MoleculeInformation(s1);
var m2 = new MoleculeInformation(s2);
_sbmlInformation.MoleculeInformation.Add(m);
_sbmlInformation.MoleculeInformation.Add(m2);
//SRef
var s1Ref = _reaction.createReactant();
s1Ref.setSpecies("s1");
s1Ref.setStoichiometry(1);
var s2Ref = _reaction.createProduct();
s2Ref.setSpecies("s2");
s2Ref.setStoichiometry(2);
_reaction.addProduct(s2Ref);
//Modifier
var mod = _reaction.createModifier();
mod.setId("mod");
mod.setName("mod");
mod.setSpecies("s1");
//Kinetic Law
var kl = _reaction.createKineticLaw();
kl.setId("kl");
kl.setMath(libsbml.parseFormula("2*3"));
}
/// <summary>
/// Creates a Molecule.
/// </summary>
private void CreateMolecule(Species species, string name, bool existant)
{
if (existant)
{
name = name + _counter;
_counter++;
}
var mbuilder = _moleculeBuilderFactory.Create(MoleculeBuildingBlock.FormulaCache)
.WithName(name)
.WithDescription(SBMLConstants.SBML_NOTES + species.getNotesString() + species.getId());
var molInfo = new MoleculeInformation(species, mbuilder);
_sbmlInformation.MoleculeInformation.Add(molInfo);
var container = GetContainerFromCompartment_(species.getCompartment());
if (container != null)
{
molInfo.AddContainer(container);
}
MoleculeBuildingBlock.Add(mbuilder);
}
