/// <summary>
/// Creates a "standard" MoBi reaction by a given one compartment reaction.
/// </summary>
private void CreateStandardReaction(Reaction sbmlReaction, Model model)
{
var reactionBuilder = ObjectBaseFactory.Create <IReactionBuilder>()
.WithName(sbmlReaction.getId())
.WithDescription(sbmlReaction.getNotesString());
CreateModifiers(sbmlReaction, reactionBuilder, String.Empty, model);
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(reactionBuilder.AddParameter);
}
if (sbmlReaction.isSetKineticLaw())
{
CreateKineticLaw(sbmlReaction.getKineticLaw(), reactionBuilder, false);
}
CreateProducts(sbmlReaction, reactionBuilder, model);
CreateEducts(sbmlReaction, reactionBuilder, model);
if (reactionBuilder != null)
{
ReactionBuilderList.Add(reactionBuilder);
}
}
/// <summary>
/// Creates the Kinetic Formula for a passive Transport.
/// </summary>
private void CreateKinetic(Reaction sbmlReaction, ITransportBuilder passiveTransport)
{
_astHandler.NeedAbsolutePath = true;
var formula = sbmlReaction.getKineticLaw() == null
? ObjectBaseFactory.Create <ExplicitFormula>().WithFormulaString(String.Empty)
: _astHandler.Parse(sbmlReaction.getKineticLaw().getMath(), sbmlReaction.getId(), _sbmlProject, _sbmlInformation);
if (formula == null)
{
passiveTransport.Formula = ObjectBaseFactory.Create <ExplicitFormula>()
.WithFormulaString(String.Empty)
.WithName(SBMLConstants.DEFAULT_FORMULA_NAME);
}
else
{
passiveTransport.Formula = formula;
_passiveTransportBuildingBlock.FormulaCache.Add(formula);
}
}
public void test_L3_Reaction_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Reaction r = new Reaction(sbmlns);
assertTrue( r.getTypeCode() == libsbml.SBML_REACTION );
assertTrue( r.getMetaId() == "" );
assertTrue( r.getNotes() == null );
assertTrue( r.getAnnotation() == null );
assertTrue( r.getLevel() == 3 );
assertTrue( r.getVersion() == 1 );
assertTrue( r.getNamespaces() != null );
assertTrue( r.getNamespaces().getLength() == 2 );
assertTrue( r.getId() == "" );
assertTrue( r.getName() == "" );
assertTrue( r.getCompartment() == "" );
assertTrue( r.getFast() == false );
assertTrue( r.getReversible() == true );
assertEquals( false, r.isSetId() );
assertEquals( false, r.isSetName() );
assertEquals( false, r.isSetCompartment() );
assertEquals( false, r.isSetFast() );
assertEquals( false, r.isSetReversible() );
r = null;
}
/// <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);
}
/// <summary>
/// Creates for each compartment of the SBML Reaction one "Ghostreaction" to import multicompartment reactions.
/// </summary>
private void CreateGhostReactions(Reaction sbmlReaction, Dictionary <string, List <SpeciesReference> > eductCompartmentMoleculeDictionary, Dictionary <string, List <SpeciesReference> > productCompartmentMoleculeDictionary, Model model)
{
var usedProducts = new List <string>();
foreach (var keyValuePair in eductCompartmentMoleculeDictionary)
{
var reactionBuilder = ObjectBaseFactory.Create <IReactionBuilder>()
.WithName(sbmlReaction.getId() + "_" + keyValuePair.Key + "_ghostReaction")
.WithDescription(sbmlReaction.getNotesString());
CreateModifiers(sbmlReaction, reactionBuilder, keyValuePair.Key, model);
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(reactionBuilder.AddParameter);
}
CreateKineticLaw(sbmlReaction.getKineticLaw(), reactionBuilder, true);
var compartmentName = keyValuePair.Key;
if (!_sbmlInformation.DummyNameContainerDictionary.ContainsValue(compartmentName))
{
return;
}
var dummyMolecule = _sbmlInformation.DummyNameContainerDictionary.FirstOrDefault(x => x.Value == compartmentName).Key;
reactionBuilder.AddModifier(dummyMolecule);
foreach (var species in keyValuePair.Value)
{
var reactionPartner = CreateReactionPartner(species, model);
if (reactionPartner != null)
{
reactionBuilder.AddEduct(reactionPartner);
}
}
if (productCompartmentMoleculeDictionary.ContainsKey(keyValuePair.Key))
{
usedProducts.Add(keyValuePair.Key);
var productsInThisCompartment = productCompartmentMoleculeDictionary[keyValuePair.Key];
foreach (var product in productsInThisCompartment)
{
var reactionPartner = CreateReactionPartner(product, model);
if (reactionPartner != null)
{
reactionBuilder.AddProduct(reactionPartner);
}
}
}
ReactionBuilderList.Add(reactionBuilder);
}
foreach (var keyValuePair in productCompartmentMoleculeDictionary)
{
if (usedProducts.Contains(keyValuePair.Key))
{
continue;
}
var reactionBuilder = ObjectBaseFactory.Create <IReactionBuilder>()
.WithName(sbmlReaction.getId() + "_" + keyValuePair.Key + "_ghostReaction")
.WithDescription(sbmlReaction.getNotesString());
CreateModifiers(sbmlReaction, reactionBuilder, keyValuePair.Key, model);
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(reactionBuilder.AddParameter);
}
CreateKineticLaw(sbmlReaction.getKineticLaw(), reactionBuilder, true);
var compartmentName = keyValuePair.Key;
if (!_sbmlInformation.DummyNameContainerDictionary.ContainsValue(compartmentName))
{
return;
}
var dummyMolecule = _sbmlInformation.DummyNameContainerDictionary.FirstOrDefault(x => x.Value == compartmentName).Key;
reactionBuilder.AddModifier(dummyMolecule);
foreach (var species in keyValuePair.Value)
{
var reactionPartner = CreateReactionPartner(species, model);
if (reactionPartner != null)
{
reactionBuilder.AddProduct(reactionPartner);
}
}
ReactionBuilderList.Add(reactionBuilder);
}
}
public void test_Model_getReaction()
{
Reaction r1 = new Reaction(2,4);
Reaction r2 = new Reaction(2,4);
r1.setId( "reaction_1");
r2.setId( "reaction_2");
M.addReaction(r1);
M.addReaction(r2);
assertTrue( M.getNumReactions() == 2 );
r1 = M.getReaction(0);
r2 = M.getReaction(1);
assertTrue(( "reaction_1" == r1.getId() ));
assertTrue(( "reaction_2" == r2.getId() ));
}
public void test_Reaction_copyConstructor()
{
Reaction o1 = new Reaction(2,4);
o1.setId("c");
assertTrue( o1.getId() == "c" );
KineticLaw kl = new KineticLaw(2,4);
kl.setMath(libsbml.parseFormula("1"));
o1.setKineticLaw(kl);
kl = null;
assertTrue( o1.isSetKineticLaw() == true );
assertNotEquals(o1.getKineticLaw(),null);
Reaction o2 = new Reaction(o1);
assertTrue( o2.getId() == "c" );
assertTrue( o2.isSetKineticLaw() == true );
assertNotEquals(o2.getKineticLaw(),null);
assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() );
o2 = null;
o1 = null;
}
public void test_Reaction_clone()
{
Reaction o1 = new Reaction(2,4);
o1.setId("c");
assertTrue( o1.getId() == "c" );
KineticLaw kl = new KineticLaw(2,4);
o1.setKineticLaw(kl);
kl = null;
assertTrue( o1.isSetKineticLaw() == true );
assertNotEquals(o1.getKineticLaw(),null);
Reaction o2 = o1.clone();
assertTrue( o2.getId() == "c" );
assertTrue( o2.isSetKineticLaw() == true );
assertNotEquals(o2.getKineticLaw(),null);
assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() );
o2 = null;
o1 = null;
}
