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);
}
}
/// <summary> Takes an object which subclasses IChemObject, e.g.Molecule, and will read
/// this (from file, database, internet etc). If the specific implementation
/// does not support a specific IChemObject it will throw an Exception.
///
/// </summary>
/// <param name="object"> The object that subclasses
/// IChemObject
/// </param>
/// <returns> The IChemObject read
/// </returns>
/// <exception cref="CDKException">
/// </exception>
public override IChemObject read(IChemObject object_Renamed)
{
if (object_Renamed is IReaction)
{
return((IChemObject)readReaction(object_Renamed.Builder));
}
else if (object_Renamed is IChemModel)
{
IChemModel model = object_Renamed.Builder.newChemModel();
ISetOfReactions reactionSet = object_Renamed.Builder.newSetOfReactions();
reactionSet.addReaction(readReaction(object_Renamed.Builder));
model.SetOfReactions = reactionSet;
return(model);
}
else if (object_Renamed is IChemFile)
{
IChemFile chemFile = object_Renamed.Builder.newChemFile();
IChemSequence sequence = object_Renamed.Builder.newChemSequence();
sequence.addChemModel((IChemModel)read(object_Renamed.Builder.newChemModel()));
chemFile.addChemSequence(sequence);
return(chemFile);
}
else
{
throw new CDKException("Only supported are Reaction and ChemModel, and not " + object_Renamed.GetType().FullName + ".");
}
}
public virtual void createIDs(ISetOfReactions reactionSet)
{
IReaction[] reactions = reactionSet.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
createIDs(reactions[i]);
}
}
public static void removeElectronContainer(ISetOfReactions set_Renamed, IElectronContainer electrons)
{
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
ReactionManipulator.removeElectronContainer(reaction, electrons);
}
}
public static void removeAtomAndConnectedElectronContainers(ISetOfReactions set_Renamed, IAtom atom)
{
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
ReactionManipulator.removeAtomAndConnectedElectronContainers(reaction, atom);
}
}
public static void setAtomProperties(ISetOfReactions set_Renamed, System.Object propKey, System.Object propVal)
{
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
ReactionManipulator.setAtomProperties(reaction, propKey, propVal);
}
}
public static void removeAtomAndConnectedElectronContainers(ISetOfReactions set_Renamed, IAtom atom)
{
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
ReactionManipulator.removeAtomAndConnectedElectronContainers(reaction, atom);
}
}
public static void removeElectronContainer(ISetOfReactions set_Renamed, IElectronContainer electrons)
{
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
ReactionManipulator.removeElectronContainer(reaction, electrons);
}
}
public static int getBondCount(ISetOfReactions set_Renamed)
{
int count = 0;
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
count += ReactionManipulator.getBondCount(reactions[i]);
}
return count;
}
/// <deprecated> This method has a serious performace impact. Try to use
/// other methods.
/// </deprecated>
public static IAtomContainer getAllInOneContainer(ISetOfReactions set_Renamed)
{
IAtomContainer container = set_Renamed.Builder.newAtomContainer();
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
container.add(ReactionManipulator.getAllInOneContainer(reaction));
}
return container;
}
public static System.Collections.IList getAllChemObjects(ISetOfReactions set_Renamed)
{
System.Collections.ArrayList list = new System.Collections.ArrayList();
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
list.AddRange(ReactionManipulator.getAllChemObjects(reaction));
}
return(list);
}
public static System.Collections.ArrayList getAllIDs(ISetOfReactions set_Renamed)
{
System.Collections.ArrayList IDlist = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
IDlist.AddRange(ReactionManipulator.getAllIDs(reaction));
}
return(IDlist);
}
public static int getBondCount(ISetOfReactions set_Renamed)
{
int count = 0;
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
count += ReactionManipulator.getBondCount(reactions[i]);
}
return(count);
}
public static IReaction getRelevantReaction(IChemModel chemModel, IAtom atom)
{
IReaction reaction = null;
if (chemModel.SetOfReactions != null)
{
ISetOfReactions reactionSet = chemModel.SetOfReactions;
reaction = SetOfReactionsManipulator.getRelevantReaction(reactionSet, atom);
}
return(reaction);
}
public static ISetOfMolecules getAllMolecules(ISetOfReactions set_Renamed)
{
ISetOfMolecules moleculeSet = set_Renamed.Builder.newSetOfMolecules();
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
moleculeSet.add(ReactionManipulator.getAllMolecules(reaction));
}
return(moleculeSet);
}
//protected internal LoggingTool logger;
/// <summary> Basic contructor</summary>
public ChemFileCDO(IChemFile file)
{
//logger = new LoggingTool(this);
currentChemFile = file;
currentChemSequence = file.Builder.newChemSequence();
currentChemModel = file.Builder.newChemModel();
currentSetOfMolecules = file.Builder.newSetOfMolecules();
currentSetOfReactions = null;
currentReaction = null;
currentMolecule = file.Builder.newMolecule();
atomEnumeration = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
}
/// <deprecated> This method has a serious performace impact. Try to use
/// other methods.
/// </deprecated>
public static IAtomContainer getAllInOneContainer(ISetOfReactions set_Renamed)
{
IAtomContainer container = set_Renamed.Builder.newAtomContainer();
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
container.add(ReactionManipulator.getAllInOneContainer(reaction));
}
return(container);
}
public static IAtomContainer getRelevantAtomContainer(ISetOfReactions set_Renamed, IBond bond)
{
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
IAtomContainer container = ReactionManipulator.getRelevantAtomContainer(reaction, bond);
if (container != null)
{
// a match!
return(container);
}
}
return(null);
}
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 virtual void createIDs(IChemModel model)
{
ICrystal crystal = model.Crystal;
if (crystal != null)
{
createIDs(crystal);
}
ISetOfMolecules moleculeSet = model.SetOfMolecules;
if (moleculeSet != null)
{
createIDs(moleculeSet);
}
ISetOfReactions reactionSet = model.SetOfReactions;
if (reactionSet != null)
{
createIDs(reactionSet);
}
}
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);
}
//protected internal LoggingTool logger;
/// <summary> Basic contructor</summary>
public ChemFileCDO(IChemFile file)
{
//logger = new LoggingTool(this);
currentChemFile = file;
currentChemSequence = file.Builder.newChemSequence();
currentChemModel = file.Builder.newChemModel();
currentSetOfMolecules = file.Builder.newSetOfMolecules();
currentSetOfReactions = null;
currentReaction = null;
currentMolecule = file.Builder.newMolecule();
atomEnumeration = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
}
public static System.Collections.ArrayList getAllIDs(ISetOfReactions set_Renamed)
{
System.Collections.ArrayList IDlist = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
IDlist.AddRange(ReactionManipulator.getAllIDs(reaction));
}
return IDlist;
}
/// <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(ISetOfReactions set_Renamed)
{
return SetOfMoleculesManipulator.getAllAtomContainers(getAllMolecules(set_Renamed));
}
/// <summary> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void startObject(System.String objectType)
{
//logger.debug("START:" + objectType);
if (objectType.Equals("Molecule"))
{
if (currentChemModel == null)
currentChemModel = currentChemFile.Builder.newChemModel();
if (currentSetOfMolecules == null)
currentSetOfMolecules = currentChemFile.Builder.newSetOfMolecules();
currentMolecule = currentChemFile.Builder.newMolecule();
}
else if (objectType.Equals("Atom"))
{
currentAtom = currentChemFile.Builder.newAtom("H");
//logger.debug("Atom # " + numberOfAtoms);
numberOfAtoms++;
}
else if (objectType.Equals("Bond"))
{
bond_id = null;
bond_stereo = -99;
}
else if (objectType.Equals("Animation"))
{
currentChemSequence = currentChemFile.Builder.newChemSequence();
}
else if (objectType.Equals("Frame"))
{
currentChemModel = currentChemFile.Builder.newChemModel();
}
else if (objectType.Equals("SetOfMolecules"))
{
currentSetOfMolecules = currentChemFile.Builder.newSetOfMolecules();
currentMolecule = currentChemFile.Builder.newMolecule();
}
else if (objectType.Equals("Crystal"))
{
currentMolecule = currentChemFile.Builder.newCrystal(currentMolecule);
}
else if (objectType.Equals("a-axis") || objectType.Equals("b-axis") || objectType.Equals("c-axis"))
{
crystal_axis_x = 0.0;
crystal_axis_y = 0.0;
crystal_axis_z = 0.0;
}
else if (objectType.Equals("SetOfReactions"))
{
currentSetOfReactions = currentChemFile.Builder.newSetOfReactions();
}
else if (objectType.Equals("Reaction"))
{
if (currentSetOfReactions == null)
startObject("SetOfReactions");
currentReaction = currentChemFile.Builder.newReaction();
}
else if (objectType.Equals("Reactant"))
{
if (currentReaction == null)
startObject("Reaction");
currentMolecule = currentChemFile.Builder.newMolecule();
}
else if (objectType.Equals("Product"))
{
if (currentReaction == null)
startObject("Reaction");
currentMolecule = currentChemFile.Builder.newMolecule();
}
}
/// <summary> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void startObject(System.String objectType)
{
//logger.debug("START:" + objectType);
if (objectType.Equals("Molecule"))
{
if (currentChemModel == null)
{
currentChemModel = currentChemFile.Builder.newChemModel();
}
if (currentSetOfMolecules == null)
{
currentSetOfMolecules = currentChemFile.Builder.newSetOfMolecules();
}
currentMolecule = currentChemFile.Builder.newMolecule();
}
else if (objectType.Equals("Atom"))
{
currentAtom = currentChemFile.Builder.newAtom("H");
//logger.debug("Atom # " + numberOfAtoms);
numberOfAtoms++;
}
else if (objectType.Equals("Bond"))
{
bond_id = null;
bond_stereo = -99;
}
else if (objectType.Equals("Animation"))
{
currentChemSequence = currentChemFile.Builder.newChemSequence();
}
else if (objectType.Equals("Frame"))
{
currentChemModel = currentChemFile.Builder.newChemModel();
}
else if (objectType.Equals("SetOfMolecules"))
{
currentSetOfMolecules = currentChemFile.Builder.newSetOfMolecules();
currentMolecule = currentChemFile.Builder.newMolecule();
}
else if (objectType.Equals("Crystal"))
{
currentMolecule = currentChemFile.Builder.newCrystal(currentMolecule);
}
else if (objectType.Equals("a-axis") || objectType.Equals("b-axis") || objectType.Equals("c-axis"))
{
crystal_axis_x = 0.0;
crystal_axis_y = 0.0;
crystal_axis_z = 0.0;
}
else if (objectType.Equals("SetOfReactions"))
{
currentSetOfReactions = currentChemFile.Builder.newSetOfReactions();
}
else if (objectType.Equals("Reaction"))
{
if (currentSetOfReactions == null)
{
startObject("SetOfReactions");
}
currentReaction = currentChemFile.Builder.newReaction();
}
else if (objectType.Equals("Reactant"))
{
if (currentReaction == null)
{
startObject("Reaction");
}
currentMolecule = currentChemFile.Builder.newMolecule();
}
else if (objectType.Equals("Product"))
{
if (currentReaction == null)
{
startObject("Reaction");
}
currentMolecule = currentChemFile.Builder.newMolecule();
}
}
public static IAtomContainer getRelevantAtomContainer(ISetOfReactions set_Renamed, IBond bond)
{
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
IAtomContainer container = ReactionManipulator.getRelevantAtomContainer(reaction, bond);
if (container != null)
{
// a match!
return container;
}
}
return null;
}
public static void setAtomProperties(ISetOfReactions set_Renamed, System.Object propKey, System.Object propVal)
{
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
ReactionManipulator.setAtomProperties(reaction, propKey, propVal);
}
}
public static System.Collections.IList getAllChemObjects(ISetOfReactions set_Renamed)
{
System.Collections.ArrayList list = new System.Collections.ArrayList();
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
list.AddRange(ReactionManipulator.getAllChemObjects(reaction));
}
return list;
}
public virtual void createIDs(ISetOfReactions reactionSet)
{
IReaction[] reactions = reactionSet.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
createIDs(reactions[i]);
}
}
public static ISetOfMolecules getAllMolecules(ISetOfReactions set_Renamed)
{
ISetOfMolecules moleculeSet = set_Renamed.Builder.newSetOfMolecules();
IReaction[] reactions = set_Renamed.Reactions;
for (int i = 0; i < reactions.Length; i++)
{
IReaction reaction = reactions[i];
moleculeSet.add(ReactionManipulator.getAllMolecules(reaction));
}
return moleculeSet;
}
