|
public getReactant ( long n ) : |
||
| n | long | |
| return | ||
/// <summary>
/// Saves educts of a SBML reaction into a dictionary, containing their compartment and SpeciesReference.
/// </summary>
private Dictionary <string, List <SpeciesReference> > ComputeEducts(Reaction sbmlReaction, Model model)
{
var eductCompartmentMoleculeDictionary = new Dictionary <string, List <SpeciesReference> >();
for (long i = 0; i < sbmlReaction.getNumReactants(); i++)
{
var reactant = sbmlReaction.getReactant(i);
var reactantSpecies = GetSpeciesById(reactant.getSpecies(), model);
var compartment = reactantSpecies.getCompartment();
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != reactantSpecies.getId())))
{
continue;
}
if (!eductCompartmentMoleculeDictionary.ContainsKey(compartment))
{
eductCompartmentMoleculeDictionary[compartment] = new List <SpeciesReference> {
reactant
}
}
;
else
{
eductCompartmentMoleculeDictionary[compartment].Add(reactant);
}
}
return(eductCompartmentMoleculeDictionary);
}
/// <summary>
/// A passive Transport is created when two Species with the same name are reacting with
/// each other.
/// </summary>
private bool IsPassiveTransport(Reaction sbmlReaction, Model model)
{
var educt = sbmlReaction.getReactant(0).getSpecies();
var product = sbmlReaction.getProduct(0).getSpecies();
var eductSpecies = GetSpeciesById(educt, model);
var productSpecies = GetSpeciesById(product, model);
if (eductSpecies.getName() != productSpecies.getName())
{
return(false);
}
var molinfoEduct = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Any(s => s == educt));
var molinfoProduct = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Any(s => s == product));
if (molinfoEduct == null)
{
return(false);
}
if (molinfoProduct == null)
{
return(false);
}
var reactantMolecule = molinfoEduct.GetMoleculeBuilder();
var productMolecule = molinfoProduct.GetMoleculeBuilder();
return(reactantMolecule == productMolecule);
}
/// <summary>
/// Creates the Educts of the MoBi reaction.
/// </summary>
private void CreateEducts(Reaction sbmlReaction, IReactionBuilder reactionBuilder, Model model)
{
for (long i = 0; i < sbmlReaction.getNumReactants(); i++)
{
var educt = CreateReactionPartner(sbmlReaction.getReactant(i), model);
if (educt != null)
{
reactionBuilder.AddEduct(educt);
}
}
}
/// <summary>
/// Checks if all reaction partners are in the same compartment.
/// </summary>
private bool IsMultiCompartmentReaction(Reaction sbmlReaction, Model model)
{
var compartment = String.Empty;
for (long i = 0; i < sbmlReaction.getNumReactants(); i++)
{
var x = sbmlReaction.getReactant(i).getSpecies();
var species = GetSpeciesById(x, model);
if (compartment == String.Empty)
{
compartment = species.getCompartment();
}
else
{
if (compartment != species.getCompartment())
{
return(true);
}
}
}
for (long i = 0; i < sbmlReaction.getNumProducts(); i++)
{
var x = sbmlReaction.getProduct(i).getSpecies();
var species = GetSpeciesById(x, model);
if (compartment == String.Empty)
{
compartment = species.getCompartment();
}
else
{
if (compartment != species.getCompartment())
{
return(true);
}
}
}
return(false);
}
public void test_SpeciesReference_Reactant_parent_create()
{
Reaction r = new Reaction(2,4);
SpeciesReference sr = r.createReactant();
ListOf lo = r.getListOfReactants();
assertTrue( lo == r.getReactant(0).getParentSBMLObject() );
assertTrue( lo == sr.getParentSBMLObject() );
assertTrue( r == lo.getParentSBMLObject() );
}
public void test_SpeciesReference_Reactant_parent_add()
{
SpeciesReference sr = new SpeciesReference(2,4);
Reaction r = new Reaction(2,4);
sr.setSpecies("s");
r.addReactant(sr);
sr = null;
ListOf lo = r.getListOfReactants();
assertTrue( lo == r.getReactant(0).getParentSBMLObject() );
assertTrue( r == lo.getParentSBMLObject() );
}
/// <summary>
/// Imports a SBML Reaction by creating a passive Transport.
/// </summary>
private void CreatePassiveTransport(Reaction sbmlReaction, Model model)
{
var reactant = sbmlReaction.getReactant(0).getSpecies();
var product = sbmlReaction.getProduct(0).getSpecies();
var reactantSpecies = GetSpeciesById(reactant, model);
var productSpecies = GetSpeciesById(product, model);
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != reactant)))
{
return;
}
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != product)))
{
return;
}
var molInfoReactant = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Contains(reactant));
var molInfoProduct = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Contains(product));
if (molInfoProduct == null)
{
return;
}
if (molInfoReactant == null)
{
return;
}
//must be the same Molecule
if (molInfoReactant.GetMoleculeBuilder() != molInfoProduct.GetMoleculeBuilder())
{
CreateErrorMessage();
}
var passiveTransport = ObjectBaseFactory.Create <ITransportBuilder>().WithName(sbmlReaction.getId());
passiveTransport.ForAll = false;
if (molInfoReactant.GetMoleculeBuilderName() == null)
{
return;
}
passiveTransport.MoleculeList.AddMoleculeName(molInfoReactant.GetMoleculeBuilderName());
var reactantCompartment = GetContainerFromCompartment_(molInfoReactant.GetCompartment(reactantSpecies));
var productCompartment = GetContainerFromCompartment_(molInfoProduct.GetCompartment(productSpecies));
if (reactantCompartment != null && productCompartment != null)
{
var reactantMatchTag = new MatchTagCondition(reactantCompartment.Name);
var productMatchTag = new MatchTagCondition(productCompartment.Name);
passiveTransport.SourceCriteria.Add(reactantMatchTag);
passiveTransport.TargetCriteria.Add(productMatchTag);
}
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(passiveTransport.AddParameter);
}
CreateKinetic(sbmlReaction, passiveTransport);
AddNeighbourhood(reactantCompartment, productCompartment, model);
_passiveTransportBuildingBlock.Add(passiveTransport);
}
public void test_SpeciesReference_Reactant_ancestor_create()
{
Reaction r = new Reaction(2,4);
SpeciesReference sr = r.createReactant();
ListOf lo = r.getListOfReactants();
assertTrue( sr.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( sr.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( sr.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( sr.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null );
SpeciesReference obj = r.getReactant(0);
assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null );
}
public void test_SpeciesReference_Reactant_ancestor_add()
{
SpeciesReference sr = new SpeciesReference(2,4);
Reaction r = new Reaction(2,4);
sr.setSpecies("s");
r.addReactant(sr);
sr = null;
ListOf lo = r.getListOfReactants();
SpeciesReference obj = r.getReactant(0);
assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null );
}