public void TestFusedRingFragments()
{
var search = new RingSearch(spiro);
var fused = search.FusedRingFragments();
Assert.AreEqual(0, fused.Count());
}
public void TestFusedRingFragments()
{
var mock_cyclicSearch = new Mock <ICyclicVertexSearch>();
var mock_container = new Mock <IAtomContainer>();
var mock_builder = new Mock <IChemObjectBuilder>();
var mock_atom = new Mock <IAtom>();
RingSearch ringSearch = new RingSearch(mock_container.Object, mock_cyclicSearch.Object);
mock_cyclicSearch.Setup(n => n.Fused()).Returns(new int[][] { new[] { 0, 1 }, new[] { 2 } });
mock_container.Setup(n => n.Builder).Returns(mock_builder.Object);
mock_builder.Setup(n => n.NewAtomContainer(It.IsAny <IEnumerable <IAtom> >(), It.IsAny <IEnumerable <IBond> >())).Returns(new Mock <IAtomContainer>().Object);
mock_container.Setup(n => n.Bonds).Returns(new List <IBond>());
mock_container.Setup(n => n.Atoms[It.IsAny <int>()]).Returns(new Mock <IAtom>().Object);
ringSearch.FusedRingFragments().ToReadOnlyList();
mock_cyclicSearch.Verify(n => n.Fused(), Times.Once());
// atoms were accessed
mock_container.Verify(n => n.Atoms[0], Times.Once());
mock_container.Verify(n => n.Atoms[1], Times.Once());
mock_container.Verify(n => n.Atoms[2], Times.Once());
// builder was invoked
mock_builder.Verify(n => n.NewAtomContainer(It.IsAny <IEnumerable <IAtom> >(), It.IsAny <IEnumerable <IBond> >()), Times.Exactly(2));
}
public void TestFusedRingFragments()
{
var search = new RingSearch(hexaphenylene);
var fused = search.FusedRingFragments().ToReadOnlyList();
Assert.AreEqual(1, fused.Count);
Assert.AreEqual(hexaphenylene.Atoms.Count, fused[0].Atoms.Count);
Assert.AreEqual(hexaphenylene.Bonds.Count, fused[0].Bonds.Count);
}
public void TestFusedRingFragments()
{
var ringSearch = new RingSearch(fusedRings);
var fragments = ringSearch.FusedRingFragments().ToReadOnlyList();
Assert.AreEqual(1, fragments.Count);
IAtomContainer fragment = fragments[0];
foreach (var atom in fusedRings.Atoms)
{
Assert.IsTrue(fragment.Contains(atom));
}
foreach (var bond in fusedRings.Bonds)
{
Assert.IsTrue(fragment.Contains(bond));
}
}
static void Main(string[] args)
{
{
#region
// construct the search for a given molecule, if an adjacency list
// representation (int[][]) is available this can be passed to the
// constructor for improved performance
IAtomContainer container = TestMoleculeFactory.MakeAlphaPinene();
RingSearch ringSearch = new RingSearch(container);
// indices of cyclic vertices
int[] cyclic = ringSearch.Cyclic();
// iterate over fused systems (atom indices)
foreach (int[] fused in ringSearch.Fused())
{
// ...
}
// iterate over isolated rings (atom indices)
foreach (int[] isolated in ringSearch.Isolated())
{
// ...
}
// convenience methods for getting the fragments
IAtomContainer fragments = ringSearch.RingFragments();
foreach (IAtomContainer fragment in ringSearch.FusedRingFragments())
{
// ...
}
foreach (IAtomContainer fragment in ringSearch.IsolatedRingFragments())
{
// ...
}
#endregion
}
{
#region Cyclic
IAtomContainer mol = TestMoleculeFactory.MakeAlphaPinene();
RingSearch ringSearch = new RingSearch(mol);
foreach (var atom in mol.Atoms)
{
if (ringSearch.Cyclic(atom))
{
// ...
}
}
#endregion
}
{
#region Cyclic_int
IAtomContainer mol = TestMoleculeFactory.MakeAlphaPinene();
RingSearch tester = new RingSearch(mol);
int n = mol.Atoms.Count;
for (int i = 0; i < n; i++)
{
if (tester.Cyclic(i))
{
// ...
}
}
#endregion
}
{
#region Isolated
IAtomContainer biphenyl = TestMoleculeFactory.MakeBiphenyl();
RingSearch ringSearch = new RingSearch(biphenyl);
int[][] isolated = ringSearch.Isolated();
Console.WriteLine(isolated.Length); // 2 isolated rings in biphenyl
Console.WriteLine(isolated[0].Length); // 6 vertices in one benzene
Console.WriteLine(isolated[1].Length); // 6 vertices in the other benzene
#endregion
}
if (true)
{
#region Fused
IAtomContainer mol = new Smiles.SmilesParser().ParseSmiles("c1cc(cc2cc(ccc12)C3C4CC34)C6CC5CCC6(C5)");
RingSearch ringSearch = new RingSearch(mol);
int[][] fused = ringSearch.Fused();
Console.WriteLine(fused.Length); // e.g. 3 separate fused ring systems
Console.WriteLine(fused[0].Length); // e.g. 10 vertices in the first system
Console.WriteLine(fused[1].Length); // e.g. 4 vertices in the second system
Console.WriteLine(fused[2].Length); // e.g. 7 vertices in the third system
#endregion
}
}