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]); } }