public static void removeElectronContainer(IChemModel chemModel, IElectronContainer electrons)
{
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
if (crystal.contains(electrons))
{
crystal.removeElectronContainer(electrons);
}
return;
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
SetOfMoleculesManipulator.removeElectronContainer(moleculeSet, electrons);
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
SetOfReactionsManipulator.removeElectronContainer(reactionSet, electrons);
}
}
public static void removeAtomAndConnectedElectronContainers(IChemModel chemModel, IAtom atom)
{
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
if (crystal.contains(atom))
{
crystal.removeAtomAndConnectedElectronContainers(atom);
}
return;
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
SetOfMoleculesManipulator.removeAtomAndConnectedElectronContainers(moleculeSet, atom);
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
SetOfReactionsManipulator.removeAtomAndConnectedElectronContainers(reactionSet, atom);
}
}
public static IAtomContainer getRelevantAtomContainer(IReaction reaction, IBond bond)
{
IAtomContainer result = SetOfMoleculesManipulator.getRelevantAtomContainer(reaction.Reactants, bond);
if (result != null)
{
return(result);
}
return(SetOfMoleculesManipulator.getRelevantAtomContainer(reaction.Products, bond));
}
/// <summary> Returns all the AtomContainer's of a ChemModel.</summary>
public static IAtomContainer[] getAllAtomContainers(IChemModel chemModel)
{
ISetOfMolecules moleculeSet = chemModel.Builder.newSetOfMolecules();
if (chemModel.SetOfMolecules != null)
{
moleculeSet.add(chemModel.SetOfMolecules);
}
if (chemModel.SetOfReactions != null)
{
moleculeSet.add(SetOfReactionsManipulator.getAllMolecules(chemModel.SetOfReactions));
}
return(SetOfMoleculesManipulator.getAllAtomContainers(moleculeSet));
}
public static void setAtomProperties(IChemModel chemModel, System.Object propKey, System.Object propVal)
{
if (chemModel.SetOfMolecules != null)
{
SetOfMoleculesManipulator.setAtomProperties(chemModel.SetOfMolecules, propKey, propVal);
}
if (chemModel.SetOfReactions != null)
{
SetOfReactionsManipulator.setAtomProperties(chemModel.SetOfReactions, propKey, propVal);
}
if (chemModel.Crystal != null)
{
AtomContainerManipulator.setAtomProperties(chemModel.Crystal, propKey, propVal);
}
}
public static IAtomContainer getRelevantAtomContainer(IChemModel chemModel, IBond bond)
{
IAtomContainer result = null;
if (chemModel.SetOfMolecules != null)
{
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
result = SetOfMoleculesManipulator.getRelevantAtomContainer(moleculeSet, bond);
if (result != null)
{
return(result);
}
}
if (chemModel.SetOfReactions != null)
{
ISetOfReactions reactionSet = chemModel.SetOfReactions;
return(SetOfReactionsManipulator.getRelevantAtomContainer(reactionSet, bond));
}
// This should never happen.
return(null);
}
public static int getBondCount(IChemModel chemModel)
{
int count = 0;
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
count += crystal.getBondCount();
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
count += SetOfMoleculesManipulator.getBondCount(moleculeSet);
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
count += SetOfReactionsManipulator.getBondCount(reactionSet);
}
return(count);
}
/// <summary> Puts all the Molecules of this container together in one
/// AtomContainer.
///
/// </summary>
/// <returns> The AtomContainer with all the Molecules of this container
///
/// </returns>
/// <deprecated> This method has a serious performace impact. Try to use
/// other methods.
/// </deprecated>
public static IAtomContainer getAllInOneContainer(IChemModel chemModel)
{
IAtomContainer container = chemModel.Builder.newAtomContainer();
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
container.add(crystal);
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
container.add(SetOfMoleculesManipulator.getAllInOneContainer(moleculeSet));
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
container.add(SetOfReactionsManipulator.getAllInOneContainer(reactionSet));
}
return(container);
}
public static System.Collections.IList getAllChemObjects(IChemModel chemModel)
{
System.Collections.ArrayList list = new System.Collections.ArrayList();
list.Add(chemModel);
ICrystal crystal = chemModel.Crystal;
if (crystal != null)
{
list.Add(crystal);
}
ISetOfMolecules moleculeSet = chemModel.SetOfMolecules;
if (moleculeSet != null)
{
list.AddRange(SetOfMoleculesManipulator.getAllChemObjects(moleculeSet));
}
ISetOfReactions reactionSet = chemModel.SetOfReactions;
if (reactionSet != null)
{
list.AddRange(SetOfReactionsManipulator.getAllChemObjects(reactionSet));
}
return(list);
}
/// <summary> Returns all the AtomContainer's of a Reaction.</summary>
public static IAtomContainer[] getAllAtomContainers(ISetOfReactions set_Renamed)
{
return(SetOfMoleculesManipulator.getAllAtomContainers(getAllMolecules(set_Renamed)));
}
/// <summary> Returns all the AtomContainer's of a Reaction.</summary>
public static IAtomContainer[] getAllAtomContainers(IReaction reaction)
{
return(SetOfMoleculesManipulator.getAllAtomContainers(getAllMolecules(reaction)));
}