public void TestGetAllAtomContainers_IRingSet()
{
IRingSet rs = builder.NewRingSet();
rs.Add(builder.NewRing());
rs.Add(builder.NewRing());
var list = RingSetManipulator.GetAllAtomContainers(rs);
Assert.AreEqual(2, list.Count());
}
/// <summary>
/// Puts all rings of a ringSet in a single atomContainer
/// </summary>
/// <param name="ringSet">The ringSet to use</param>
/// <returns>The produced atomContainer</returns>
public static IAtomContainer GetAllInOneContainer(IRingSet ringSet)
{
IAtomContainer resultContainer = ringSet.Builder.NewAtomContainer();
IEnumerator <IAtomContainer> containers = RingSetManipulator.GetAllAtomContainers(ringSet).GetEnumerator();
while (containers.MoveNext())
{
resultContainer.Add(containers.Current);
}
return(resultContainer);
}
public void TestSort_IRingSet()
{
RingSetManipulator.Sort(ringset);
Assert.AreEqual(4, ringset.Count);
int currentSize = ringset[0].Atoms.Count;
for (int i = 1; i < ringset.Count; ++i)
{
Assert.IsTrue(ringset[i].Atoms.Count >= currentSize);
currentSize = ringset[i].Atoms.Count;
}
}
public void TestGetLargestRingSetListIRingSet()
{
var list = new List <IRingSet> {
ringset
};
var mol = TestMoleculeFactory.MakeBiphenyl();
var arf = new AllRingsFinder();
var ringSet = arf.FindAllRings(mol);
list.Add(ringSet);
Assert.AreEqual(2, RingSetManipulator.GetLargestRingSet(list).Count);
}
public void TestGetBondCount()
{
IAtomContainer mol = TestMoleculeFactory.MakeAdenine();
AllRingsFinder arf = new AllRingsFinder();
IRingSet ringSet = arf.FindAllRings(mol);
Assert.AreEqual(3, ringSet.Count);
Assert.AreEqual(20, RingSetManipulator.GetBondCount(ringSet));
mol = TestMoleculeFactory.MakeBiphenyl();
ringSet = arf.FindAllRings(mol);
Assert.AreEqual(2, ringSet.Count);
Assert.AreEqual(12, RingSetManipulator.GetBondCount(ringSet));
}
public void TestGetAtomCount_IRingSet()
{
IRingSet rs = builder.NewRingSet();
IRing ac1 = builder.NewRing();
ac1.Atoms.Add(builder.NewAtom("O"));
rs.Add(ac1);
IRing ac2 = builder.NewRing();
ac2.Atoms.Add(builder.NewAtom("C"));
ac2.Atoms.Add(builder.NewAtom("C"));
ac2.AddBond(ac2.Atoms[0], ac2.Atoms[1], BondOrder.Double);
rs.Add(ac2);
Assert.AreEqual(3, RingSetManipulator.GetAtomCount(rs));
Assert.AreEqual(1, RingSetManipulator.GetBondCount(rs));
}
/// <summary>
/// Returns the largest (number of atoms) ring set in a molecule
/// </summary>
/// <param name="ringSystems">RingSystems of a molecule</param>
/// <returns>The largestRingSet</returns>
public static IRingSet GetLargestRingSet(IEnumerable <IRingSet> ringSystems)
{
IRingSet largestRingSet = null;
int atomNumber = 0;
IAtomContainer container = null;
foreach (var ringSystem in ringSystems)
{
container = RingSetManipulator.GetAllInOneContainer(ringSystem);
if (atomNumber < container.Atoms.Count)
{
atomNumber = container.Atoms.Count;
largestRingSet = ringSystem;
}
}
return(largestRingSet);
}
public void TestRingAlreadyInSet_IRing_IRingSet()
{
IRing r1 = builder.NewRing(5, "C");
IRing r2 = builder.NewRing(3, "C");
IRingSet rs = builder.NewRingSet();
Assert.IsFalse(RingSetManipulator.RingAlreadyInSet(r1, rs));
Assert.IsFalse(RingSetManipulator.RingAlreadyInSet(r2, rs));
rs.Add(r1);
Assert.IsTrue(RingSetManipulator.RingAlreadyInSet(r1, rs));
Assert.IsFalse(RingSetManipulator.RingAlreadyInSet(r2, rs));
rs.Add(r2);
Assert.IsTrue(RingSetManipulator.RingAlreadyInSet(r1, rs));
Assert.IsTrue(RingSetManipulator.RingAlreadyInSet(r2, rs));
}
public void MarkAromatic()
{
IAtomContainer mol = TestMoleculeFactory.MakeBiphenyl();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
AllRingsFinder arf = new AllRingsFinder();
IRingSet ringSet = arf.FindAllRings(mol);
Assert.AreEqual(2, ringSet.Count);
RingSetManipulator.MarkAromaticRings(ringSet);
for (int i = 0; i < ringSet.Count; i++)
{
IRing ring = (IRing)ringSet[i];
Assert.IsTrue(ring.IsAromatic);
}
}
public void TestGetAllInOneContainer_IRingSet()
{
IAtomContainer ac = RingSetManipulator.GetAllInOneContainer(ringset);
Assert.AreEqual(10, ac.Atoms.Count);
}
public void TestGetMostComplexRing_IRingSet()
{
IRing ring = RingSetManipulator.GetMostComplexRing(ringset);
Assert.AreEqual(ring3, ring);
}
public void TestGetHeaviestRing_IRingSet_IBond()
{
IRing ring = RingSetManipulator.GetHeaviestRing(ringset, bondRing2Ring3);
Assert.AreEqual(ring2, ring);
}
public void TestIsSameRing_IRingSet_IAtom_IAtom()
{
Assert.IsTrue(RingSetManipulator.IsSameRing(ringset, ring1Atom1, ring1Atom3));
Assert.IsFalse(RingSetManipulator.IsSameRing(ringset, ring1Atom1, ring2Atom3));
}
