/// <summary> Returns all the AtomContainer's of a ChemFile.</summary>
public static IAtomContainer[] getAllAtomContainers(IChemFile file)
{
IChemSequence[] sequences = file.ChemSequences;
int acCount = 0;
System.Collections.ArrayList acArrays = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int i = 0; i < sequences.Length; i++)
{
IAtomContainer[] sequenceContainers = ChemSequenceManipulator.getAllAtomContainers(sequences[i]);
acArrays.Add(sequenceContainers);
acCount += sequenceContainers.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);
}
/// <summary> Returns a List of all IChemObject in this ChemFile.
///
/// </summary>
/// <returns> A list of all ChemObjects
/// </returns>
public static System.Collections.IList getAllChemObjects(IChemFile file)
{
System.Collections.ArrayList list = new System.Collections.ArrayList();
list.Add(file);
for (int i = 0; i < file.ChemSequenceCount; i++)
{
list.AddRange(ChemSequenceManipulator.getAllChemObjects(file.getChemSequence(i)));
}
return(list);
}
public static int getBondCount(IChemFile file)
{
int count = 0;
for (int i = 0; i < file.ChemSequenceCount; i++)
{
count += ChemSequenceManipulator.getBondCount(file.getChemSequence(i));
}
return(count);
}
/// <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(IChemFile file)
{
IAtomContainer container = file.Builder.newAtomContainer();
for (int i = 0; i < file.ChemSequenceCount; i++)
{
IChemSequence sequence = file.getChemSequence(i);
container.add(ChemSequenceManipulator.getAllInOneContainer(sequence));
}
return(container);
}
