/// <summary>
/// Creates the Local Parameters of the MoBi Reaction by the given local Parameters
/// of the SBML Reaction.
/// </summary>
private List <IParameter> CreateLocalParameters(Reaction sbmlReaction)
{
if (sbmlReaction.getKineticLaw() == null)
{
return(null);
}
if (sbmlReaction.getKineticLaw().getNumLocalParameters() <= 0)
{
return(null);
}
var parameter = new List <IParameter>();
for (long i = 0; i < sbmlReaction.getKineticLaw().getNumLocalParameters(); i++)
{
var p = sbmlReaction.getKineticLaw().getLocalParameter(i);
var formula = ObjectBaseFactory.Create <ConstantFormula>()
.WithValue(p.getValue());
var localParameter = ObjectBaseFactory.Create <IParameter>()
.WithName(p.getId())
.WithDescription(p.getNotesString())
.WithFormula(formula);
var dim = GetDimension(p);
if (dim != null)
{
localParameter.Dimension = dim;
}
if (localParameter != null)
{
parameter.Add(localParameter);
}
}
return(parameter);
}
/// <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);
}
}
private static void printReactionMath(int n, Reaction r)
{
string formula;
KineticLaw kl;
if (r.isSetKineticLaw())
{
kl = r.getKineticLaw();
if (kl.isSetMath())
{
formula = libsbml.formulaToString(kl.getMath());
Console.Write("Reaction " + n + ", formula: " + formula + Environment.NewLine);
}
}
}
public void test_KineticLaw_parent_add()
{
KineticLaw kl = new KineticLaw(2,4);
Reaction r = new Reaction(2,4);
r.setKineticLaw(kl);
assertTrue( r == r.getKineticLaw().getParentSBMLObject() );
r = null;
}
/// <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_KineticLaw_ancestor_create()
{
Reaction r = new Reaction(2,4);
KineticLaw kl = r.createKineticLaw();
assertTrue( kl.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( kl.getAncestorOfType(libsbml.SBML_DELAY) == null );
assertTrue( kl.getAncestorOfType(libsbml.SBML_MODEL) == null );
assertTrue( kl.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
KineticLaw obj = r.getKineticLaw();
assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DELAY) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
r = null;
}
public void test_KineticLaw_ancestor_add()
{
KineticLaw kl = new KineticLaw(2,4);
Reaction r = new Reaction(2,4);
r.setKineticLaw(kl);
KineticLaw obj = r.getKineticLaw();
assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r );
assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == null );
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
r = null;
}
public void test_KineticLaw_parent_add()
{
KineticLaw kl = new KineticLaw(2,4);
kl.setMath(libsbml.parseFormula("1"));
Reaction r = new Reaction(2, 4);
r.setKineticLaw(kl);
assertTrue( r == r.getKineticLaw().getParentSBMLObject() );
r = null;
}
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;
}