public void RequireAtLeastTwoProjectedSubstituents()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("O", 0, -0.71d, 1.24d));
m.Atoms.Add(Atom("C", 0, 0.00d, 0.83d));
m.Atoms.Add(Atom("O", 0, 0.71d, 1.24d));
m.Atoms.Add(Atom("C", 1, 0.00d, 0.00d));
m.Atoms.Add(Atom("C", 2, -0.67d, -0.48d));
m.Atoms.Add(Atom("C", 2, -0.41d, -1.27d));
m.Atoms.Add(Atom("C", 2, 0.41d, -1.27d));
m.Atoms.Add(Atom("N", 1, 0.67d, -0.48d));
m.AddBond(m.Atoms[6], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[0], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[2], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[6], m.Atoms[7], BondOrder.Single);
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.Haworth }).ToReadOnlyList();
Assert.IsTrue(elements.Count == 0);
}
public void ChairClockwise()
{
Assert.IsTrue(Compares.AreDeepEqual(
new Turn[] { Left, Left, Right, Left, Left, Right },
CyclicCarbohydrateRecognition.GetTurns(new Vector2[] {
new Vector2(1.7, 2.4),
new Vector2(1.3, 3.1),
new Vector2(0.5, 2.9),
new Vector2(0.2, 3.1),
new Vector2(0.1, 2.4),
new Vector2(0.9, 2.6)
})));
}
public void HaworthClockwise()
{
Assert.IsTrue(Compares.AreDeepEqual(
new Turn[] { Right, Right, Right, Right, Right, Right },
CyclicCarbohydrateRecognition.GetTurns(new Vector2[] {
new Vector2(4.1, 3.0),
new Vector2(4.8, 2.6),
new Vector2(4.8, 1.8),
new Vector2(4.1, 1.4),
new Vector2(3.3, 1.8),
new Vector2(3.3, 2.6)
})));
}
public void BoatClockwise()
{
Assert.IsTrue(Compares.AreDeepEqual(
new Turn[] { Left, Right, Right, Left, Left, Left },
CyclicCarbohydrateRecognition.GetTurns(new Vector2[] {
new Vector2(3.8, 4.8),
new Vector2(3.1, 4.2),
new Vector2(2.3, 4.2),
new Vector2(1.6, 4.9),
new Vector2(2.1, 3.8),
new Vector2(3.3, 3.8)
})));
}
public void Hexopyranose()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("O", 1, 0.00d, 2.48d));
m.Atoms.Add(Atom("C", 2, 0.71d, 2.06d));
m.Atoms.Add(Atom("C", 1, 0.71d, 1.24d));
m.Atoms.Add(Atom("O", 0, 1.43d, 0.82d));
m.Atoms.Add(Atom("C", 1, 1.43d, -0.00d));
m.Atoms.Add(Atom("O", 1, 2.14d, -0.41d));
m.Atoms.Add(Atom("C", 1, 0.71d, -0.41d));
m.Atoms.Add(Atom("O", 1, 0.71d, -1.24d));
m.Atoms.Add(Atom("C", 1, -0.00d, 0.00d));
m.Atoms.Add(Atom("O", 1, -0.71d, -0.41d));
m.Atoms.Add(Atom("C", 1, 0.00d, 0.83d));
m.Atoms.Add(Atom("O", 1, -0.71d, 1.24d));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[1], 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[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[2], 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);
Stereocenters stereocenters = new Stereocenters(m, graph, bondMap);
stereocenters.CheckSymmetry();
CyclicCarbohydrateRecognition recon = new CyclicCarbohydrateRecognition(m, graph, bondMap,
stereocenters);
Assert.IsTrue(recon.Recognise(new[] { Projection.Haworth }).Count() == 0);
}
public void HaworthFalsePositive()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 2, -0.71d, 0.41d));
m.Atoms.Add(Atom("C", 2, 0.71d, -0.41d));
m.Atoms.Add(Atom("C", 2, 0.71d, 0.41d));
m.Atoms.Add(Atom("C", 2, -0.71d, -0.41d));
m.Atoms.Add(Atom("C", 1, 0.00d, 0.82d));
m.Atoms.Add(Atom("C", 3, 0.00d, 1.65d));
m.Atoms.Add(Atom("C", 3, -0.71d, -2.06d));
m.Atoms.Add(Atom("C", 1, -0.00d, -1.65d));
m.Atoms.Add(Atom("C", 3, 0.71d, -2.06d));
m.Atoms.Add(Atom("C", 1, -0.00d, -0.83d));
m.AddBond(m.Atoms[9], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[9], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[0], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[9], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[7], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[7], m.Atoms[8], BondOrder.Single);
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.Haworth }).ToReadOnlyList();
Assert.IsTrue(elements.Count == 0);
}
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]);
}
}
public void Atp_Haworth()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("O", 0, 2.56d, -6.46d));
m.Atoms.Add(Atom("C", 1, 1.90d, -6.83d));
m.Atoms.Add(Atom("C", 1, 2.15d, -7.46d));
m.Atoms.Add(Atom("C", 1, 2.98d, -7.46d));
m.Atoms.Add(Atom("C", 1, 3.23d, -6.83d));
m.Atoms.Add(Atom("C", 2, 1.90d, -6.00d));
m.Atoms.Add(Atom("O", 0, 1.18d, -5.59d));
m.Atoms.Add(Atom("O", 1, 2.15d, -8.29d));
m.Atoms.Add(Atom("O", 1, 2.98d, -8.29d));
m.Atoms.Add(Atom("P", 0, 0.36d, -5.59d));
m.Atoms.Add(Atom("O", 0, -0.47d, -5.59d));
m.Atoms.Add(Atom("O", 0, 0.36d, -4.76d));
m.Atoms.Add(Atom("O", 1, 0.36d, -6.41d));
m.Atoms.Add(Atom("P", 0, -1.29d, -5.59d));
m.Atoms.Add(Atom("O", 0, -2.12d, -5.59d));
m.Atoms.Add(Atom("O", 0, -1.29d, -4.76d));
m.Atoms.Add(Atom("O", 1, -1.29d, -6.41d));
m.Atoms.Add(Atom("P", 0, -2.94d, -5.59d));
m.Atoms.Add(Atom("O", 1, -3.77d, -5.59d));
m.Atoms.Add(Atom("O", 0, -2.94d, -4.76d));
m.Atoms.Add(Atom("O", 1, -2.94d, -6.41d));
m.Atoms.Add(Atom("C", 0, 4.73d, -4.51d));
m.Atoms.Add(Atom("C", 0, 4.02d, -4.92d));
m.Atoms.Add(Atom("C", 0, 4.02d, -5.75d));
m.Atoms.Add(Atom("N", 0, 4.73d, -6.16d));
m.Atoms.Add(Atom("N", 0, 5.44d, -5.75d));
m.Atoms.Add(Atom("C", 1, 5.44d, -4.92d));
m.Atoms.Add(Atom("C", 1, 2.75d, -5.33d));
m.Atoms.Add(Atom("N", 0, 3.23d, -4.67d));
m.Atoms.Add(Atom("N", 2, 4.73d, -3.68d));
m.Atoms.Add(Atom("N", 0, 3.23d, -6.00d));
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[0], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[6], m.Atoms[9], BondOrder.Single);
m.AddBond(m.Atoms[9], m.Atoms[10], BondOrder.Single);
m.AddBond(m.Atoms[9], m.Atoms[11], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[9], m.Atoms[12], BondOrder.Single);
m.AddBond(m.Atoms[13], m.Atoms[14], BondOrder.Single);
m.AddBond(m.Atoms[13], m.Atoms[15], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[13], m.Atoms[16], BondOrder.Single);
m.AddBond(m.Atoms[10], m.Atoms[13], BondOrder.Single);
m.AddBond(m.Atoms[17], m.Atoms[18], BondOrder.Single);
m.AddBond(m.Atoms[17], m.Atoms[19], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[17], m.Atoms[20], BondOrder.Single);
m.AddBond(m.Atoms[14], m.Atoms[17], BondOrder.Single);
m.AddBond(m.Atoms[21], m.Atoms[22], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[22], m.Atoms[23], BondOrder.Single);
m.AddBond(m.Atoms[23], m.Atoms[24], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[24], m.Atoms[25], BondOrder.Single);
m.AddBond(m.Atoms[25], m.Atoms[26], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[21], m.Atoms[26], BondOrder.Single);
m.AddBond(m.Atoms[27], m.Atoms[28], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[22], m.Atoms[28], BondOrder.Single);
m.AddBond(m.Atoms[21], m.Atoms[29], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[30], BondOrder.Single);
m.AddBond(m.Atoms[30], m.Atoms[27], BondOrder.Single);
m.AddBond(m.Atoms[23], m.Atoms[30], BondOrder.Single);
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.Haworth }).ToReadOnlyList();
AssertTetrahedralCenter(elements[0],
m.Atoms[1],
TetrahedralStereo.AntiClockwise,
m.Atoms[5], m.Atoms[0], m.Atoms[1], m.Atoms[2]);
AssertTetrahedralCenter(elements[1],
m.Atoms[2],
TetrahedralStereo.AntiClockwise,
m.Atoms[2], m.Atoms[1], m.Atoms[7], m.Atoms[3]);
AssertTetrahedralCenter(elements[2],
m.Atoms[3],
TetrahedralStereo.AntiClockwise,
m.Atoms[3], m.Atoms[2], m.Atoms[8], m.Atoms[4]);
AssertTetrahedralCenter(elements[3],
m.Atoms[4],
TetrahedralStereo.AntiClockwise,
m.Atoms[30], m.Atoms[3], m.Atoms[4], m.Atoms[0]);
}
public void Oxpene()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 1, 1.39d, 3.65d));
m.Atoms.Add(Atom("C", 2, 2.22d, 3.65d));
m.Atoms.Add(Atom("C", 1, 2.93d, 4.07d));
m.Atoms.Add(Atom("C", 1, 0.68d, 4.07d));
m.Atoms.Add(Atom("C", 1, 1.01d, 4.63d));
m.Atoms.Add(Atom("C", 1, 2.52d, 4.64d));
m.Atoms.Add(Atom("O", 0, 1.76d, 4.89d));
m.Atoms.Add(Atom("O", 1, 0.68d, 3.24d));
m.Atoms.Add(Atom("C", 2, 1.01d, 5.45d));
m.Atoms.Add(Atom("O", 1, 0.18d, 5.45d));
m.Atoms.Add(Atom("C", 3, 2.52d, 5.46d));
m.Atoms.Add(Atom("O", 0, 2.93d, 3.24d));
m.Atoms.Add(Atom("C", 2, 1.39d, 4.48d));
m.Atoms.Add(Atom("C", 3, 2.22d, 4.48d));
m.Atoms.Add(Atom("C", 2, 3.76d, 3.24d));
m.Atoms.Add(Atom("C", 2, 4.34d, 2.66d));
m.Atoms.Add(Atom("O", 0, 5.16d, 2.66d));
m.Atoms.Add(Atom("C", 3, 5.58d, 3.37d));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[6], 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[4], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[9], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[10], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[11], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[12], BondOrder.Single);
m.AddBond(m.Atoms[12], m.Atoms[13], BondOrder.Single);
m.AddBond(m.Atoms[11], m.Atoms[14], BondOrder.Single);
m.AddBond(m.Atoms[14], m.Atoms[15], BondOrder.Single);
m.AddBond(m.Atoms[15], m.Atoms[16], BondOrder.Single);
m.AddBond(m.Atoms[16], m.Atoms[17], BondOrder.Single);
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.Haworth }).ToReadOnlyList();
AssertTetrahedralCenter(elements[0],
m.Atoms[2],
TetrahedralStereo.AntiClockwise,
m.Atoms[2], m.Atoms[1], m.Atoms[11], m.Atoms[5]);
AssertTetrahedralCenter(elements[1],
m.Atoms[5],
TetrahedralStereo.AntiClockwise,
m.Atoms[10], m.Atoms[2], m.Atoms[5], m.Atoms[6]);
AssertTetrahedralCenter(elements[2],
m.Atoms[4],
TetrahedralStereo.AntiClockwise,
m.Atoms[8], m.Atoms[6], m.Atoms[4], m.Atoms[3]);
AssertTetrahedralCenter(elements[3],
m.Atoms[3],
TetrahedralStereo.AntiClockwise,
m.Atoms[3], m.Atoms[4], m.Atoms[7], m.Atoms[0]);
AssertTetrahedralCenter(elements[4],
m.Atoms[0],
TetrahedralStereo.AntiClockwise,
m.Atoms[12], m.Atoms[3], m.Atoms[0], m.Atoms[1]);
}
public void BetaDGlucoseWithExplicitHydrogens_Haworth()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 0, 4.16d, 1.66d));
m.Atoms.Add(Atom("C", 0, 3.75d, 0.94d));
m.Atoms.Add(Atom("C", 0, 4.16d, 0.23d));
m.Atoms.Add(Atom("C", 0, 5.05d, 0.23d));
m.Atoms.Add(Atom("C", 0, 5.46d, 0.94d));
m.Atoms.Add(Atom("O", 0, 5.05d, 1.66d));
m.Atoms.Add(Atom("O", 1, 5.46d, 1.48d));
m.Atoms.Add(Atom("C", 2, 4.16d, 2.20d));
m.Atoms.Add(Atom("O", 1, 3.45d, 2.61d));
m.Atoms.Add(Atom("O", 1, 3.74d, 0.50d));
m.Atoms.Add(Atom("O", 1, 4.16d, 0.77d));
m.Atoms.Add(Atom("O", 1, 5.04d, -0.21d));
m.Atoms.Add(Atom("H", 0, 4.15d, -0.21d));
m.Atoms.Add(Atom("H", 0, 5.05d, 0.77d));
m.Atoms.Add(Atom("H", 0, 5.45d, 0.50d));
m.Atoms.Add(Atom("H", 0, 3.75d, 1.48d));
m.Atoms.Add(Atom("H", 0, 4.17d, 1.15d));
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[0], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[7], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[9], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[10], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[11], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[12], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[13], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[14], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[15], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[16], BondOrder.Single);
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.Haworth }).ToReadOnlyList();
AssertTetrahedralCenter(elements[0],
m.Atoms[1],
TetrahedralStereo.AntiClockwise,
m.Atoms[15], m.Atoms[0], m.Atoms[9], m.Atoms[2]);
AssertTetrahedralCenter(elements[1],
m.Atoms[2],
TetrahedralStereo.AntiClockwise,
m.Atoms[10], m.Atoms[1], m.Atoms[12], m.Atoms[3]);
AssertTetrahedralCenter(elements[2],
m.Atoms[3],
TetrahedralStereo.AntiClockwise,
m.Atoms[13], m.Atoms[2], m.Atoms[11], m.Atoms[4]);
AssertTetrahedralCenter(elements[3],
m.Atoms[4],
TetrahedralStereo.AntiClockwise,
m.Atoms[6], m.Atoms[3], m.Atoms[14], m.Atoms[5]);
AssertTetrahedralCenter(elements[4],
m.Atoms[0],
TetrahedralStereo.AntiClockwise,
m.Atoms[7], m.Atoms[5], m.Atoms[16], m.Atoms[1]);
}
