public void TestCyclic_Bond()
{
var mock_cyclicSearch = new Mock <ICyclicVertexSearch>();
ICyclicVertexSearch cyclicSearch = mock_cyclicSearch.Object;
var mock_container = new Mock <IAtomContainer>();
IAtomContainer container = mock_container.Object;
IAtom a1 = new Mock <IAtom>().Object;
IAtom a2 = new Mock <IAtom>().Object;
var mock_bond = new Mock <IBond>();
IBond bond = mock_bond.Object;
mock_container.Setup(n => n.Atoms.IndexOf(a1)).Returns(42);
mock_container.Setup(n => n.Atoms.IndexOf(a2)).Returns(43);
mock_bond.Setup(n => n.Begin).Returns(a1);
mock_bond.Setup(n => n.End).Returns(a2);
RingSearch ringSearch = new RingSearch(container, cyclicSearch);
ringSearch.Cyclic(bond);
// verify the number returned from getAtomNumber is passed on
mock_container.Verify(n => n.Atoms.IndexOf(a1), Times.Once());
mock_container.Verify(n => n.Atoms.IndexOf(a2), Times.Once());
mock_cyclicSearch.Verify(n => n.Cyclic(42, 43), Times.Once());
}
public void TestCyclic_Int()
{
var ringSearch = new RingSearch(fusedRings);
for (int i = 0; i < fusedRings.Atoms.Count; i++)
{
Assert.IsTrue(ringSearch.Cyclic(i));
}
}
public void TestCyclic_Int()
{
var n = spiro.Atoms.Count;
var ringSearch = new RingSearch(spiro);
for (int i = 0; i < n; i++)
{
Assert.IsTrue(ringSearch.Cyclic(i));
}
}
public void TestCyclic_Int()
{
var n = hexaphenylene.Atoms.Count;
var ringSearch = new RingSearch(hexaphenylene);
for (int i = 0; i < n; i++)
{
Assert.IsTrue(ringSearch.Cyclic(i));
}
}
public void TestCyclic_Int()
{
int n = nonCyclic.Atoms.Count;
RingSearch ringSearch = new RingSearch(nonCyclic);
for (int i = 0; i < n; i++)
{
Assert.IsFalse(ringSearch.Cyclic(i));
}
}
public void TestCyclic_Int()
{
var n = bicyclo.Atoms.Count;
var ringSearch = new RingSearch(bicyclo);
for (int i = 0; i < n; i++)
{
Assert.IsTrue(ringSearch.Cyclic(i), "all atoms should be cyclic");
}
}
public void TestCyclic()
{
var mock_cyclicSearch = new Mock <ICyclicVertexSearch>();
ICyclicVertexSearch cyclicSearch = mock_cyclicSearch.Object;
IAtomContainer container = new Mock <IAtomContainer>().Object;
RingSearch ringSearch = new RingSearch(container, cyclicSearch);
ringSearch.Cyclic();
mock_cyclicSearch.Verify(n => n.Cyclic(), Times.Once());
}
public void TestCyclic_Atom_NotFound()
{
ICyclicVertexSearch cyclicSearch = new Mock <ICyclicVertexSearch>().Object;
var mock_container = new Mock <IAtomContainer>();
IAtomContainer container = mock_container.Object;
IAtom atom = new Mock <IAtom>().Object;
mock_container.Setup(n => n.Atoms.IndexOf(It.IsAny <IAtom>())).Returns(-1);
RingSearch ringSearch = new RingSearch(container, cyclicSearch);
ringSearch.Cyclic(atom);
}
public void TestCyclic_Atom()
{
var mock_cyclicSearch = new Mock <ICyclicVertexSearch>();
ICyclicVertexSearch cyclicSearch = mock_cyclicSearch.Object;
var mock_container = new Mock <IAtomContainer>();
IAtomContainer container = mock_container.Object;
IAtom atom = new Mock <IAtom>().Object;
mock_container.Setup(n => n.Atoms.IndexOf(It.IsAny <IAtom>())).Returns(42);
RingSearch ringSearch = new RingSearch(container, cyclicSearch);
ringSearch.Cyclic(atom);
// verify the number returned from getAtomNumber is passed on
mock_container.Verify(n => n.Atoms.IndexOf(atom), Times.Once());
mock_cyclicSearch.Verify(n => n.Cyclic(42), Times.Once());
}
public void TestCyclic_Int()
{
var n = benzylbenzene.Atoms.Count;
var ringSearch = new RingSearch(benzylbenzene);
int cyclic = 0, acyclic = 0;
for (int i = 0; i < n; i++)
{
if (ringSearch.Cyclic(i))
{
cyclic++;
}
else
{
acyclic++;
}
}
// single atom not in a ring
Assert.AreEqual(1, acyclic);
Assert.AreEqual(n - 1, cyclic);
}
public void TestCyclic()
{
var ringSearch = new RingSearch(fusedRings);
Assert.AreEqual(fusedRings.Atoms.Count, ringSearch.Cyclic().Length);
}
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
}
}