/// <summary> Returns all the AtomContainer's of a ChemSequence.</summary>
public static IAtomContainer[] getAllAtomContainers(IChemSequence sequence)
{
IChemModel[] models = sequence.ChemModels;
int acCount = 0;
System.Collections.ArrayList acArrays = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int i = 0; i < models.Length; i++)
{
IAtomContainer[] modelContainers = ChemModelManipulator.getAllAtomContainers(models[i]);
acArrays.Add(modelContainers);
acCount += modelContainers.Length;
}
IAtomContainer[] containers = new IAtomContainer[acCount];
int arrayOffset = 0;
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
for (System.Collections.IEnumerator acArraysElements = acArrays.GetEnumerator(); acArraysElements.MoveNext();)
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
IAtomContainer[] modelContainers = (IAtomContainer[])acArraysElements.Current;
Array.Copy(modelContainers, 0, containers, arrayOffset, modelContainers.Length);
arrayOffset += modelContainers.Length;
}
return(containers);
}
public static int getBondCount(IChemSequence sequence)
{
int count = 0;
for (int i = 0; i < sequence.ChemModelCount; i++)
{
count += ChemModelManipulator.getBondCount(sequence.getChemModel(i));
}
return(count);
}
public static System.Collections.IList getAllChemObjects(IChemSequence sequence)
{
System.Collections.ArrayList list = new System.Collections.ArrayList();
list.Add(sequence);
for (int i = 0; i < sequence.ChemModelCount; i++)
{
list.AddRange(ChemModelManipulator.getAllChemObjects(sequence.getChemModel(i)));
}
return(list);
}
/// <summary> Puts all the Molecules of this container together in one
/// AtomCcntainer.
///
/// </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(IChemSequence sequence)
{
IAtomContainer container = sequence.Builder.newAtomContainer();
for (int i = 0; i < sequence.ChemModelCount; i++)
{
IChemModel model = sequence.getChemModel(i);
container.add(ChemModelManipulator.getAllInOneContainer(model));
}
return(container);
}