/// <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 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);
}
}
