public void RecogniseLeftHandedGlyceraldehyde()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 0, 0.80d, 1.24d));
m.Atoms.Add(Atom("C", 0, 0.80d, 0.42d));
m.Atoms.Add(Atom("O", 1, 0.09d, 1.66d));
m.Atoms.Add(Atom("O", 0, 1.52d, 1.66d));
m.Atoms.Add(Atom("O", 0, -0.02d, 0.42d));
m.Atoms.Add(Atom("C", 2, 0.80d, -0.41d));
m.Atoms.Add(Atom("H", 1, 1.63d, 0.42d));
m.Atoms.Add(Atom("O", 1, 1.52d, -0.82d));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[3], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[1], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[7], 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(1, elements.Count);
AssertTetrahedralCenter(elements[0],
m.Atoms[1],
TetrahedralStereo.AntiClockwise,
m.Atoms[0], m.Atoms[6], m.Atoms[5], m.Atoms[4]);
}
public void CreateCenterWithThreeNeighbors_left()
{
IAtom focus = Atom("C", 0, 0.80d, 0.42d);
IAtom north = Atom("C", 0, 0.80d, 1.24d);
IAtom south = Atom("C", 2, 0.80d, -0.41d);
IAtom west = Atom("O", 1, -0.02d, 0.42d);
IBond[] bonds = new IBond[]
{
new Bond(focus, south),
new Bond(focus, north),
new Bond(focus, west)
};
ITetrahedralChirality element = FischerRecognition.NewTetrahedralCenter(focus,
bonds);
Assert.AreSame(focus, element.ChiralAtom);
Assert.AreEqual(TetrahedralStereo.AntiClockwise, element.Stereo);
Assert.AreSame(north, element.Ligands[0]);
Assert.AreSame(focus, element.Ligands[1]);
Assert.AreSame(south, element.Ligands[2]);
Assert.AreSame(west, element.Ligands[3]);
}
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 DoNotCreateCenterWhenEastAndWestAreMissing()
{
IAtom focus = Atom("C", 0, 0.80d, 0.42d);
IAtom north = Atom("C", 0, 0.80d, 1.24d);
IAtom south = Atom("C", 2, 0.80d, -0.41d);
IBond[] bonds = new IBond[] {
new Bond(focus, north),
new Bond(focus, south)
};
ITetrahedralChirality element = FischerRecognition.NewTetrahedralCenter(focus,
bonds);
Assert.IsNull(element);
}
public void DoNotCreateCenterWhenSouthIsMissing()
{
IAtom focus = Atom("C", 0, 0.80d, 0.42d);
IAtom north = Atom("C", 0, 0.80d, 1.24d);
IAtom east = Atom("O", 1, 1.63d, 0.42d);
IAtom west = Atom("H", 0, -0.02d, 0.42d);
IBond[] bonds = new IBond[] {
new Bond(focus, north),
new Bond(focus, west),
new Bond(focus, east)
};
ITetrahedralChirality element = FischerRecognition.NewTetrahedralCenter(focus,
bonds);
Assert.IsNull(element);
}
public void HorizontalBondsMustBeTerminal()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 0, 12.71d, -16.51d));
m.Atoms.Add(Atom("C", 1, 12.30d, -17.22d));
m.Atoms.Add(Atom("C", 1, 11.47d, -17.22d));
m.Atoms.Add(Atom("C", 1, 11.06d, -16.51d));
m.Atoms.Add(Atom("C", 1, 11.47d, -15.79d));
m.Atoms.Add(Atom("C", 1, 12.30d, -15.79d));
m.Atoms.Add(Atom("O", 1, 13.54d, -17.33d));
m.Atoms.Add(Atom("C", 0, 13.54d, -16.51d));
m.Atoms.Add(Atom("C", 0, 14.36d, -16.51d));
m.Atoms.Add(Atom("O", 1, 14.77d, -17.22d));
m.Atoms.Add(Atom("O", 0, 14.77d, -15.79d));
m.Atoms.Add(Atom("C", 3, 13.54d, -15.68d));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[5], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[1], m.Atoms[2], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[2], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Double, BondStereo.EZByCoordinates);
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);
m.AddBond(m.Atoms[8], m.Atoms[9], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[10], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[0], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[11], m.Atoms[7], BondOrder.Single);
EdgeToBondMap bondMap = EdgeToBondMap.WithSpaceFor(m);
int[][] graph = GraphUtil.ToAdjList(m, bondMap);
FischerRecognition recogniser = new FischerRecognition(m,
graph,
bondMap,
Stereocenters.Of(m));
Assert.IsTrue(recogniser.Recognise(new[] { Projection.Fischer }).Count() == 0);
}
public void DoNotCreateCenterWhenRotated()
{
IAtom focus = Atom("C", 0, 0.44d, 3.30d);
IAtom north = Atom("C", 3, -0.16d, 3.86d);
IAtom east = Atom("O", 1, 1.00d, 3.90d);
IAtom south = Atom("C", 3, 1.05d, 2.74d);
IAtom west = Atom("H", 0, -0.12d, 2.70d);
IBond[] bonds = new IBond[] {
new Bond(focus, west),
new Bond(focus, north),
new Bond(focus, south),
new Bond(focus, east)
};
ITetrahedralChirality element = FischerRecognition.NewTetrahedralCenter(focus,
bonds);
Assert.IsNull(element);
}
public void ObtainNonPerfectCardinalBonds()
{
IAtom focus = Atom("C", 0, -0.40d, 3.37d);
IAtom north = Atom("C", 0, -0.43d, 4.18d);
IAtom east = Atom("O", 1, 0.44d, 3.33d);
IAtom south = Atom("C", 2, -0.42d, 2.65d);
IAtom west = Atom("H", 0, -1.21d, 3.36d);
IBond[] expected = new IBond[] {
new Bond(focus, north),
new Bond(focus, east),
new Bond(focus, south),
new Bond(focus, west)
};
IBond[] actual = FischerRecognition.CardinalBonds(focus,
new IBond[] { expected[1],
expected[2],
expected[3],
expected[0] }
);
Assert.IsTrue(Compares.AreDeepEqual(actual, expected));
}
public void ObtainCardinalBonds()
{
IAtom focus = Atom("C", 0, 0.80d, 0.42d);
IAtom north = Atom("C", 0, 0.80d, 1.24d);
IAtom east = Atom("O", 1, 1.63d, 0.42d);
IAtom south = Atom("C", 2, 0.80d, -0.41d);
IAtom west = Atom("H", 0, -0.02d, 0.42d);
IBond[] expected = new IBond[] {
new Bond(focus, north),
new Bond(focus, east),
new Bond(focus, south),
new Bond(focus, west)
};
IBond[] actual = FischerRecognition.CardinalBonds(focus,
new IBond[] { expected[1],
expected[2],
expected[3],
expected[0] }
);
Assert.IsTrue(Compares.AreDeepEqual(actual, expected));
}
public void IgnoreCyclicStereocenters()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 0, 6.87d, -5.59d));
m.Atoms.Add(Atom("C", 0, 6.87d, -6.61d));
m.Atoms.Add(Atom("C", 0, 7.82d, -5.62d));
m.Atoms.Add(Atom("C", 0, 6.87d, -4.59d));
m.Atoms.Add(Atom("O", 0, 8.18d, -6.34d));
m.Atoms.Add(Atom("C", 0, 7.62d, -6.91d));
m.Atoms.Add(Atom("C", 0, 5.90d, -5.59d));
m.Atoms.Add(Atom("C", 0, 8.39d, -5.06d));
m.Atoms.Add(Atom("C", 0, 5.60d, -4.80d));
m.Atoms.Add(Atom("C", 2, 6.16d, -4.24d));
m.Atoms.Add(Atom("O", 0, 8.22d, -4.29d));
m.Atoms.Add(Atom("C", 2, 6.10d, -6.90d));
m.Atoms.Add(Atom("C", 2, 5.54d, -6.29d));
m.Atoms.Add(Atom("C", 2, 7.46d, -4.07d));
m.Atoms.Add(Atom("O", 0, 7.79d, -7.72d));
m.Atoms.Add(Atom("O", 0, 9.18d, -5.29d));
m.Atoms.Add(Atom("O", 1, 6.87d, -7.44d));
m.Atoms.Add(Atom("C", 3, 6.76d, -3.77d));
m.Atoms.Add(Atom("C", 3, 4.82d, -5.07d));
m.Atoms.Add(Atom("C", 3, 5.19d, -4.08d));
m.Atoms.Add(Atom("H", 0, 8.64d, -5.76d));
m.Atoms.Add(Atom("H", 0, 5.08d, -5.69d));
m.AddBond(m.Atoms[1], m.Atoms[0], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[0], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[7], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[9], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[10], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[11], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[12], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[13], m.Atoms[3], BondOrder.Single);
m.AddBond(m.Atoms[14], m.Atoms[5], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[15], m.Atoms[7], BondOrder.Double, BondStereo.EZByCoordinates);
m.AddBond(m.Atoms[1], m.Atoms[16], BondOrder.Single, BondStereo.Up);
m.AddBond(m.Atoms[3], m.Atoms[17], BondOrder.Single, BondStereo.Up);
m.AddBond(m.Atoms[18], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[19], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[20], BondOrder.Single, BondStereo.Down);
m.AddBond(m.Atoms[6], m.Atoms[21], BondOrder.Single, BondStereo.Down);
m.AddBond(m.Atoms[5], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[11], m.Atoms[12], BondOrder.Single);
m.AddBond(m.Atoms[10], m.Atoms[13], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[9], BondOrder.Single);
EdgeToBondMap bondMap = EdgeToBondMap.WithSpaceFor(m);
int[][] graph = GraphUtil.ToAdjList(m, bondMap);
FischerRecognition recogniser = new FischerRecognition(m,
graph,
bondMap,
Stereocenters.Of(m));
Assert.IsTrue(recogniser.Recognise(new[] { Projection.Fischer }).Count() == 0);
}
