/// <summary>
/// Get the total number of bonds inside an IChemFile.
/// </summary>
/// <param name="file">The IChemFile object.</param>
/// <returns>The number of Bond object inside.</returns>
public static int GetBondCount(IChemFile file)
{
int count = 0;
for (int i = 0; i < file.Count; i++)
{
count += ChemSequenceManipulator.GetBondCount(file[i]);
}
return(count);
}
public void TestGetAllIDs_IChemSequence()
{
Assert.AreEqual(0, ChemSequenceManipulator.GetAllIDs(chemSequence).Count());
IDCreator.CreateIDs(chemSequence);
var allIDs = ChemSequenceManipulator.GetAllIDs(chemSequence);
Assert.AreEqual(18, ChemSequenceManipulator.GetAllIDs(chemSequence).Count());
var uniq = new HashSet <string>(allIDs);
Assert.AreEqual(12, uniq.Count);
}
/// <summary>
/// Returns all the AtomContainer's of a ChemFile.
/// </summary>
public static IEnumerable <IAtomContainer> GetAllAtomContainers(IChemFile file)
{
foreach (var sequence in file)
{
foreach (var ac in ChemSequenceManipulator.GetAllAtomContainers(sequence))
{
yield return(ac);
}
}
yield break;
}
/// <summary>
/// Returns a List of all IChemObject inside a ChemFile.
/// </summary>
/// <returns>A list of all ChemObjects</returns>
public static IEnumerable <IChemObject> GetAllChemObjects(IChemFile file)
{
//list.Add(file); // should not add the original file
foreach (var sequence in file)
{
yield return(sequence);
foreach (var o in ChemSequenceManipulator.GetAllChemObjects(sequence))
{
yield return(o);
}
}
yield break;
}
public static IEnumerable <string> GetAllIDs(IChemFile file)
{
if (file.Id != null)
{
yield return(file.Id);
}
foreach (var sequence in file)
{
foreach (var id in ChemSequenceManipulator.GetAllIDs(sequence))
{
yield return(id);
}
}
yield break;
}
public void TestGetAllChemObjects_IChemSequence()
{
var list = ChemSequenceManipulator.GetAllChemObjects(chemSequence);
int molCount = 0;
int molSetCount = 0;
int reactionCount = 0;
int reactionSetCount = 0;
int chemModelCount = 0;
foreach (var o in list)
{
//if (o is IAtom) ++atomCount;
//if (o is IBond) ++bondCount;
if (o is IAtomContainer)
{
++molCount;
}
else if (o is IChemObjectSet <IAtomContainer> )
{
++molSetCount;
}
else if (o is IReaction)
{
++reactionCount;
}
else if (o is IReactionSet)
{
++reactionSetCount;
}
else if (o is IChemModel)
{
++chemModelCount;
}
else
{
Assert.Fail("Unexpected Object of type " + o.GetType());
}
}
//Assert.AreEqual(3, atomCount);
//Assert.AreEqual(1, bondCount);
Assert.AreEqual(2, molCount);
Assert.AreEqual(1, molSetCount);
Assert.AreEqual(1, reactionCount);
Assert.AreEqual(1, reactionSetCount);
Assert.AreEqual(2, chemModelCount);
}
public void TestGetBondCount_IChemSequence()
{
int count = ChemSequenceManipulator.GetBondCount(chemSequence);
Assert.AreEqual(2, count);
}
public void TestGetAllAtomContainers_IChemSequence()
{
var list = ChemSequenceManipulator.GetAllAtomContainers(chemSequence);
Assert.AreEqual(4, list.Count());
}