public void S_penta_2_3_diene_expl_h()
{
var m = new AtomContainer();
m.Atoms.Add(new Atom("C"));
m.Atoms.Add(new Atom("C"));
m.Atoms.Add(new Atom("C"));
m.Atoms.Add(new Atom("C"));
m.Atoms.Add(new Atom("C"));
m.Atoms.Add(new Atom("H"));
m.Atoms.Add(new Atom("H"));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[2], BondOrder.Double);
m.AddBond(m.Atoms[2], m.Atoms[3], BondOrder.Double);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[6], BondOrder.Single);
var atoms = new int[][] { new[] { 0, 5, 6, 4 }, new[] { 5, 0, 6, 4 }, new[] { 5, 0, 4, 6 }, new[] { 0, 5, 4, 6 }, new[] { 4, 6, 5, 0 }, new[] { 4, 6, 0, 5 }, new[] { 6, 4, 0, 5 }, new[] { 6, 4, 5, 0 }, };
var stereos = new TetrahedralStereo[] { TetrahedralStereo.Clockwise, TetrahedralStereo.AntiClockwise, TetrahedralStereo.Clockwise, TetrahedralStereo.AntiClockwise, TetrahedralStereo.Clockwise, TetrahedralStereo.AntiClockwise, TetrahedralStereo.Clockwise, TetrahedralStereo.AntiClockwise };
for (int i = 0; i < atoms.Length; i++)
{
var element = new ExtendedTetrahedral(m.Atoms[2], new IAtom[] { m.Atoms[atoms[i][0]], m.Atoms[atoms[i][1]], m.Atoms[atoms[i][2]], m.Atoms[atoms[i][3]] }, stereos[i]);
m.SetStereoElements(new[] { element });
Assert.AreEqual("CC(=[C@]=C(C)[H])[H]", Convert(m, SmiFlavors.Stereo).ToSmiles());
}
}
public void Mannitol()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 2, -0.53d, 6.25d));
m.Atoms.Add(Atom("C", 1, -0.53d, 5.42d));
m.Atoms.Add(Atom("O", 1, 0.18d, 6.66d));
m.Atoms.Add(Atom("O", 1, -1.36d, 5.42d));
m.Atoms.Add(Atom("C", 1, -0.53d, 4.60d));
m.Atoms.Add(Atom("O", 1, -1.36d, 4.60d));
m.Atoms.Add(Atom("C", 1, -0.53d, 3.77d));
m.Atoms.Add(Atom("O", 1, 0.29d, 3.77d));
m.Atoms.Add(Atom("C", 1, -0.53d, 2.95d));
m.Atoms.Add(Atom("O", 1, 0.29d, 2.95d));
m.Atoms.Add(Atom("C", 2, -0.53d, 2.12d));
m.Atoms.Add(Atom("O", 1, 0.05d, 1.54d));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[6], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[6], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[9], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[10], BondOrder.Single);
m.AddBond(m.Atoms[10], m.Atoms[11], BondOrder.Single);
EdgeToBondMap bondMap = EdgeToBondMap.WithSpaceFor(m);
int[][] graph = GraphUtil.ToAdjList(m, bondMap);
FischerRecognition recogniser = new FischerRecognition(m,
graph,
bondMap,
Stereocenters.Of(m));
var elements = recogniser.Recognise(new[] { Projection.Fischer }).ToReadOnlyList();
Assert.AreEqual(4, elements.Count);
AssertTetrahedralCenter(elements[0],
m.Atoms[1],
TetrahedralStereo.AntiClockwise,
m.Atoms[0], m.Atoms[1], m.Atoms[4], m.Atoms[3]);
AssertTetrahedralCenter(elements[1],
m.Atoms[4],
TetrahedralStereo.AntiClockwise,
m.Atoms[1], m.Atoms[4], m.Atoms[6], m.Atoms[5]);
AssertTetrahedralCenter(elements[2],
m.Atoms[6],
TetrahedralStereo.AntiClockwise,
m.Atoms[4], m.Atoms[7], m.Atoms[8], m.Atoms[6]);
AssertTetrahedralCenter(elements[3],
m.Atoms[8],
TetrahedralStereo.AntiClockwise,
m.Atoms[6], m.Atoms[9], m.Atoms[10], m.Atoms[8]);
m.SetStereoElements(elements);
}
public void S_penta_2_3_diene_impl_h()
{
var m = new AtomContainer();
m.Atoms.Add(new Atom("C"));
m.Atoms.Add(new Atom("C"));
m.Atoms.Add(new Atom("C"));
m.Atoms.Add(new Atom("C"));
m.Atoms.Add(new Atom("C"));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[2], BondOrder.Double);
m.AddBond(m.Atoms[2], m.Atoms[3], BondOrder.Double);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Single);
var element = new ExtendedTetrahedral(m.Atoms[2], new IAtom[] { m.Atoms[0], m.Atoms[1], m.Atoms[3], m.Atoms[4] }, TetrahedralStereo.Clockwise);
m.SetStereoElements(new[] { element });
Assert.AreEqual("CC=[C@@]=CC", Convert(m, SmiFlavors.Stereo).ToSmiles());
}
public void BetaDGlucose_Chair_Rotated()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 1, -0.77d, 10.34d));
m.Atoms.Add(Atom("C", 1, 0.03d, 10.13d));
m.Atoms.Add(Atom("O", 0, 0.83d, 10.34d));
m.Atoms.Add(Atom("C", 1, 1.24d, 9.63d));
m.Atoms.Add(Atom("C", 1, 0.44d, 9.84d));
m.Atoms.Add(Atom("C", 1, -0.35d, 9.63d));
m.Atoms.Add(Atom("O", 1, 0.86d, 9.13d));
m.Atoms.Add(Atom("O", 1, 2.04d, 9.84d));
m.Atoms.Add(Atom("C", 2, -0.68d, 10.54d));
m.Atoms.Add(Atom("O", 1, -0.68d, 11.37d));
m.Atoms.Add(Atom("O", 1, -1.48d, 9.93d));
m.Atoms.Add(Atom("O", 1, -1.15d, 9.84d));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[0], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[9], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[10], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[11], BondOrder.Single);
Vector2 center = GeometryUtil.Get2DCenter(m);
GeometryUtil.Rotate(m, center, Vectors.DegreeToRadian(-80));
for (int i = 0; i < 30; i++)
{
GeometryUtil.Rotate(m, center, Vectors.DegreeToRadian(5));
EdgeToBondMap bondMap = EdgeToBondMap.WithSpaceFor(m);
int[][] graph = GraphUtil.ToAdjList(m, bondMap);
Stereocenters stereocenters = new Stereocenters(m, graph, bondMap);
stereocenters.CheckSymmetry();
CyclicCarbohydrateRecognition recon = new CyclicCarbohydrateRecognition(m, graph, bondMap,
stereocenters);
var elements = recon.Recognise(new[] { Projection.Chair }).ToReadOnlyList();
m.SetStereoElements(elements);
AssertTetrahedralCenter(elements[0],
m.Atoms[1],
TetrahedralStereo.Clockwise,
m.Atoms[8], m.Atoms[0], m.Atoms[1], m.Atoms[2]);
AssertTetrahedralCenter(elements[1],
m.Atoms[3],
TetrahedralStereo.Clockwise,
m.Atoms[7], m.Atoms[2], m.Atoms[3], m.Atoms[4]);
AssertTetrahedralCenter(elements[2],
m.Atoms[4],
TetrahedralStereo.Clockwise,
m.Atoms[4], m.Atoms[3], m.Atoms[6], m.Atoms[5]);
AssertTetrahedralCenter(elements[3],
m.Atoms[5],
TetrahedralStereo.Clockwise,
m.Atoms[11], m.Atoms[4], m.Atoms[5], m.Atoms[0]);
AssertTetrahedralCenter(elements[4],
m.Atoms[0],
TetrahedralStereo.Clockwise,
m.Atoms[0], m.Atoms[5], m.Atoms[10], m.Atoms[1]);
}
}