public override void EndElement(CMLStack xpath, XElement element)
{
var local = element.Name.LocalName;
switch (local)
{
case "reaction":
CurrentReactionSet.Add(CurrentReaction);
CurrentChemModel.ReactionSet = CurrentReactionSet;
break;
case "reactionList":
CurrentChemModel.ReactionSet = CurrentReactionSet;
/* FIXME: this should be when document is closed! */
break;
case "reactant":
CurrentReaction.Reactants.Add(CurrentMolecule);
break;
case "product":
CurrentReaction.Products.Add(CurrentMolecule);
break;
case "substance":
CurrentReaction.Agents.Add(CurrentMolecule);
break;
case "molecule":
Debug.WriteLine("Storing Molecule");
//if the current molecule exists in the currentMoleculeSet means that is a reference in these.
if (CurrentMoleculeSet.GetMultiplier(CurrentMolecule) == -1)
{
base.StoreData();
}
// do nothing else but store atom/bond information
break;
default:
base.EndElement(xpath, element);
break;
}
}
public override void EndElement(CMLStack xpath, XElement element)
{
string name = element.Name.LocalName;
// OLD +++++++++++++++++++++++++++++++++++++++++++++
switch (name)
{
case "list":
if (connectionTable && !isBond)
{
Debug.WriteLine("End Connection Table");
connectionTable = false;
// OLD +++++++++++++++++++++++++++++++++++++++++++++
}
break;
case "molecule":
StoreData();
if (xpath.Count == 1)
{
// cdo.EndObject("Molecule");
if (CurrentMolecule is IAtomContainer)
{
Debug.WriteLine("Adding molecule to set");
CurrentMoleculeSet.Add(CurrentMolecule);
Debug.WriteLine($"#mols in set: {CurrentMoleculeSet.Count}");
}
else if (CurrentMolecule is ICrystal)
{
Debug.WriteLine("Adding crystal to chemModel");
CurrentChemModel.Crystal = (ICrystal)CurrentMolecule;
CurrentChemSequence.Add(CurrentChemModel);
}
}
break;
}
isELSYM = false;
isBond = false;
}
public override void StartElement(CMLStack xpath, XElement element)
{
if (string.Equals("reaction", element.Name.LocalName, StringComparison.Ordinal))
{
// cdo.StartObject("Reaction");
if (CurrentReactionSet == null)
{
CurrentReactionSet = CurrentChemFile.Builder.NewReactionSet();
}
CurrentReaction = CurrentChemFile.Builder.NewReaction();
string id = AttGetValue(element.Attributes(), "id");
if (id != null)
{
CurrentReaction.Id = id;
}
// cdo.SetObjectProperty("Reaction", "id", id);
}
else if (string.Equals("reactionList", element.Name.LocalName, StringComparison.Ordinal))
{
// cdo.StartObject("ReactionSet");
CurrentReactionSet = CurrentChemFile.Builder.NewReactionSet();
string id = AttGetValue(element.Attributes(), "id");
if (id != null)
{
CurrentReactionSet.Id = id;
}
// cdo.SetObjectProperty("reactionList", "id", id);
}
else if (string.Equals("reactant", element.Name.LocalName, StringComparison.Ordinal))
{
// cdo.StartObject("Reactant");
if (CurrentReaction == null)
{
if (CurrentReactionSet == null)
{
CurrentReactionSet = CurrentChemFile.Builder.NewReactionSet();
}
CurrentReaction = CurrentChemFile.Builder.NewReaction();
}
CurrentMolecule = CurrentChemFile.Builder.NewAtomContainer();
#if DEBUG
objectType = "Reactant";
#endif
string id = AttGetValue(element.Attributes(), "id");
if (id != null)
{
CurrentMolecule.Id = id;
}
else
{
string ref_ = AttGetValue(element.Attributes(), "ref");
if (ref_ != null)
{
CurrentMolecule.Id = ref_;
}
}
// cdo.SetObjectProperty("Reactant", "id", id);
}
else if (string.Equals("product", element.Name.LocalName, StringComparison.Ordinal))
{
// cdo.StartObject("Product");
if (CurrentReaction == null)
{
if (CurrentReactionSet == null)
{
CurrentReactionSet = CurrentChemFile.Builder.NewReactionSet();
}
CurrentReaction = CurrentChemFile.Builder.NewReaction();
}
CurrentMolecule = CurrentChemFile.Builder.NewAtomContainer();
#if DEBUG
objectType = "Product";
#endif
string id = AttGetValue(element.Attributes(), "id");
if (id != null)
{
CurrentMolecule.Id = id;
}
else
{
string ref_ = AttGetValue(element.Attributes(), "ref");
if (ref_ != null)
{
CurrentMolecule.Id = ref_;
}
}
// cdo.SetObjectProperty("Product", "id", id);
}
else if (string.Equals("substance", element.Name.LocalName, StringComparison.Ordinal))
{
// cdo.StartObject("Agent");
if (CurrentReaction == null)
{
if (CurrentReactionSet == null)
{
CurrentReactionSet = CurrentChemFile.Builder.NewReactionSet();
}
CurrentReaction = CurrentChemFile.Builder.NewReaction();
}
CurrentMolecule = CurrentChemFile.Builder.NewAtomContainer();
#if DEBUG
objectType = "Agent";
#endif
string id = AttGetValue(element.Attributes(), "id");
if (id != null)
{
CurrentMolecule.Id = id;
}
else
{
string ref_ = AttGetValue(element.Attributes(), "ref");
if (ref_ != null)
{
CurrentMolecule.Id = ref_;
}
}
// cdo.SetObjectProperty("Agent", "id", id);
}
else if (string.Equals("molecule", element.Name.LocalName, StringComparison.Ordinal))
{
// clear existing molecule data
base.NewMolecule();
string id = AttGetValue(element.Attributes(), "id");
if (id != null)
{
// check for existing molecule of that id
IAtomContainer existing = GetMoleculeFromID(CurrentMoleculeSet, id);
if (existing != null)
{
CurrentMolecule = existing;
}
else
{
CurrentMolecule.Id = id;
}
}
else
{
string ref_ = AttGetValue(element.Attributes(), "ref");
if (ref_ != null)
{
IAtomContainer atomC = GetMoleculeFromID(CurrentMoleculeSet, ref_);
// if there was no molecule create a new one for the reference. this
// happens when the reaction is defined before the molecule set
if (atomC == null)
{
atomC = CurrentChemFile.Builder.NewAtomContainer();
atomC.Id = ref_;
CurrentMoleculeSet.Add(atomC);
}
base.CurrentMolecule = atomC;
}
}
}
else
{
base.StartElement(xpath, element);
}
}
