public void UnspecifiedMarkedOnDifferentLigands()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("R", 0, 0.00, -0.00));
m.Atoms.Add(Atom("C", 2, 1.30, -0.75));
m.Atoms.Add(Atom("N", 0, 2.60, -0.00));
m.Atoms.Add(Atom("C", 0, 3.90, -0.75));
m.Atoms.Add(Atom("C", 2, 5.20, -0.00));
m.Atoms.Add(Atom("C", 2, 6.50, -0.75));
m.Atoms.Add(Atom("C", 3, 7.79, -0.00));
m.Atoms.Add(Atom("C", 2, 3.90, -2.25));
m.Atoms.Add(Atom("C", 2, 5.20, -3.00));
m.Atoms.Add(Atom("N", 2, 5.20, -4.50));
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.Double);
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[6], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[7], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[9], BondOrder.Single);
NonplanarBonds.Assign(m);
int wavyCount = 0;
foreach (var bond in m.Bonds)
{
if (bond.Stereo == BondStereo.UpOrDown)
{
wavyCount++;
}
}
Assert.AreEqual(1, wavyCount);
}
public void DontMarkUnspecifiedForLinearEqualChains()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("R", 0, 0.00, -0.00));
m.Atoms.Add(Atom("C", 2, 1.30, -0.75));
m.Atoms.Add(Atom("N", 0, 2.60, -0.00));
m.Atoms.Add(Atom("C", 0, 3.90, -0.75));
m.Atoms.Add(Atom("C", 2, 5.20, -0.00));
m.Atoms.Add(Atom("C", 2, 6.50, -0.75));
m.Atoms.Add(Atom("C", 3, 7.79, -0.00));
m.Atoms.Add(Atom("C", 2, 3.90, -2.25));
m.Atoms.Add(Atom("C", 2, 5.20, -3.00));
m.Atoms.Add(Atom("C", 3, 5.20, -4.50));
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.Double);
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[6], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[7], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[8], m.Atoms[9], BondOrder.Single);
NonplanarBonds.Assign(m);
foreach (var bond in m.Bonds)
{
Assert.AreEqual(BondStereo.None, bond.Stereo);
}
}
public void MarkUnspecifiedForCyclicLigands()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("R", 0, -4.22, 3.05));
m.Atoms.Add(Atom("C", 2, -2.92, 2.30));
m.Atoms.Add(Atom("N", 0, -1.62, 3.05));
m.Atoms.Add(Atom("C", 0, -0.32, 2.30));
m.Atoms.Add(Atom("C", 2, -0.33, 0.80));
m.Atoms.Add(Atom("C", 2, 0.97, 0.05));
m.Atoms.Add(Atom("C", 2, 2.27, 0.80));
m.Atoms.Add(Atom("C", 2, 2.27, 2.30));
m.Atoms.Add(Atom("C", 2, 0.97, 3.05));
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.Double);
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[6], BondOrder.Single);
m.AddBond(m.Atoms[6], m.Atoms[7], BondOrder.Single);
m.AddBond(m.Atoms[7], m.Atoms[8], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[8], BondOrder.Single);
Cycles.MarkRingAtomsAndBonds(m);
NonplanarBonds.Assign(m);
int wavyCount = 0;
foreach (var bond in m.Bonds)
{
if (bond.Stereo == BondStereo.UpOrDown)
{
wavyCount++;
}
}
Assert.AreEqual(1, wavyCount);
}
public void Anticlockwise_2()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 0, -0.96d, -1.04d));
m.Atoms.Add(Atom("C", 2, 0.18d, -0.08d));
m.Atoms.Add(Atom("C", 2, -0.08d, 1.40d));
m.Atoms.Add(Atom("C", 3, 1.07d, 2.36d));
m.Atoms.Add(Atom("C", 2, -1.71d, -2.34d));
m.Atoms.Add(Atom("C", 3, -2.11d, -0.08d));
m.Atoms.Add(Atom("C", 1, -0.21d, -2.34d));
m.Atoms.Add(Atom("C", 3, 1.08d, -3.09d));
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[0], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[6], m.Atoms[7], BondOrder.Single);
m.StereoElements.Add(new TetrahedralChirality(m.Atoms[0], new IAtom[] { m.Atoms[1], m.Atoms[4], m.Atoms[5], m.Atoms[6] }, TetrahedralStereo.AntiClockwise));
NonplanarBonds.Assign(m);
Assert.AreEqual(BondStereo.Down, m.Bonds[0].Stereo);
Assert.AreEqual(BondStereo.None, m.Bonds[3].Stereo);
Assert.AreEqual(BondStereo.Up, m.Bonds[4].Stereo);
Assert.AreEqual(BondStereo.None, m.Bonds[5].Stereo);
}
public void DontMarkTetrahedralCentresWithDoubleBondsAsUnspecified()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 3, 2.598, 1.500));
m.Atoms.Add(Atom("S", 0, 2.598, -0.000));
m.Atoms.Add(Atom("C", 1, 1.299, -0.750));
m.Atoms.Add(Atom("C", 3, 0.000, 0.000));
m.Atoms.Add(Atom("C", 2, 3.897, -0.750));
m.Atoms.Add(Atom("C", 3, 5.196, -0.000));
m.AddBond(m.Atoms[1], m.Atoms[0], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[2], BondOrder.Double);
m.AddBond(m.Atoms[2], 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.StereoElements.Add(
new TetrahedralChirality(
m.Atoms[1],
new IAtom[] { m.Atoms[0], m.Atoms[1], m.Atoms[2], m.Atoms[4] },
TetrahedralStereo.AntiClockwise));
NonplanarBonds.Assign(m);
Assert.AreNotEqual(BondStereo.UpOrDown, m.Bonds[0].Stereo);
Assert.AreNotEqual(BondStereo.UpOrDown, m.Bonds[2].Stereo);
Assert.AreNotEqual(BondStereo.UpOrDown, m.Bonds[3].Stereo);
}
public void DontCrossEtheneDoubleBond()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 2, 0.000, 0.000));
m.Atoms.Add(Atom("C", 2, 1.299, -0.750));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Double);
NonplanarBonds.Assign(m);
Assert.AreEqual(BondStereo.None, m.Bonds[0].Stereo);
}
public void MarkBut2eneWithWavyBond()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 3, 0.000, 0.000));
m.Atoms.Add(Atom("C", 1, 1.299, -0.750));
m.Atoms.Add(Atom("C", 1, 2.598, -0.000));
m.Atoms.Add(Atom("C", 3, 3.897, -0.750));
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.Single);
NonplanarBonds.Assign(m);
Assert.AreEqual(BondStereo.UpOrDown, m.Bonds[0].Stereo);
}
public void DontMarkTerminalBonds()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 3, 0.000, 0.000));
m.Atoms.Add(Atom("C", 0, 1.299, -0.750));
m.Atoms.Add(Atom("C", 2, 2.598, -0.000));
m.Atoms.Add(Atom("C", 3, 3.897, -0.750));
m.Atoms.Add(Atom("O", 0, 1.299, -2.250));
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[1], m.Atoms[4], BondOrder.Double);
NonplanarBonds.Assign(m);
Assert.AreEqual(BondStereo.None, m.Bonds[0].Stereo);
Assert.AreEqual(BondStereo.None, m.Bonds[1].Stereo);
Assert.AreEqual(BondStereo.None, m.Bonds[2].Stereo);
}
public void Anticlockwise_implH_1()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 1, 0.00d, 1.50d));
m.Atoms.Add(Atom("C", 3, 0.00d, 0.00d));
m.Atoms.Add(Atom("N", 2, -1.30d, 2.25d));
m.Atoms.Add(Atom("O", 1, 1.30d, 2.25d));
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.Single);
m.StereoElements.Add(new TetrahedralChirality(
m.Atoms[0],
new IAtom[] { m.Atoms[0], m.Atoms[1], m.Atoms[2], m.Atoms[3] },
TetrahedralStereo.AntiClockwise));
NonplanarBonds.Assign(m);
Assert.AreEqual(BondStereo.None, m.Bonds[0].Stereo);
Assert.AreEqual(BondStereo.Up, m.Bonds[1].Stereo);
Assert.AreEqual(BondStereo.None, m.Bonds[2].Stereo);
}
public void DontMarkGuanidineAsUnspecified()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("R", 0, 0.00, 0.00));
m.Atoms.Add(Atom("C", 2, 1.30, -0.75));
m.Atoms.Add(Atom("N", 0, 2.60, -0.00));
m.Atoms.Add(Atom("C", 0, 3.90, -0.75));
m.Atoms.Add(Atom("N", 2, 5.20, -0.00));
m.Atoms.Add(Atom("N", 2, 3.90, -2.25));
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.Double);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[5], BondOrder.Single);
NonplanarBonds.Assign(m);
foreach (var bond in m.Bonds)
{
Assert.AreEqual(BondStereo.None, bond.Stereo);
}
}
public void DontMarkRingBondsInBezeneAsUnspecified()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 1, -1.299, 0.750));
m.Atoms.Add(Atom("C", 1, 0.000, 1.500));
m.Atoms.Add(Atom("C", 1, 1.299, 0.750));
m.Atoms.Add(Atom("C", 1, 1.299, -0.750));
m.Atoms.Add(Atom("C", 1, 0.000, -1.500));
m.Atoms.Add(Atom("C", 1, -1.299, -0.750));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Double);
m.AddBond(m.Atoms[1], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[3], BondOrder.Double);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[4], m.Atoms[5], BondOrder.Double);
m.AddBond(m.Atoms[0], m.Atoms[5], BondOrder.Single);
NonplanarBonds.Assign(m);
foreach (var bond in m.Bonds)
{
Assert.AreEqual(BondStereo.None, bond.Stereo);
}
}
public void NonPlanarBondsForClockwsieExtendedTetrahedral()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 3, -1.56d, 0.78d));
m.Atoms.Add(Atom("C", 0, -1.13d, 1.49d));
m.Atoms.Add(Atom("C", 0, -0.31d, 1.47d));
m.Atoms.Add(Atom("C", 0, 0.52d, 1.46d));
m.Atoms.Add(Atom("C", 3, 0.94d, 2.17d));
m.Atoms.Add(Atom("H", 0, 0.92d, 0.74d));
m.Atoms.Add(Atom("H", 0, -1.53d, 2.21d));
m.AddBond(m.Atoms[0], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[2], BondOrder.Double, BondStereo.None);
m.AddBond(m.Atoms[2], m.Atoms[3], BondOrder.Double, BondStereo.None);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[5], BondOrder.Single);
m.StereoElements.Add(new ExtendedTetrahedral(m.Atoms[2], new IAtom[] { m.Atoms[0], m.Atoms[6], m.Atoms[4], m.Atoms[5] }, TetrahedralStereo.Clockwise));
NonplanarBonds.Assign(m);
Assert.AreEqual(BondStereo.Up, m.GetBond(m.Atoms[1], m.Atoms[0]).Stereo);
Assert.AreEqual(BondStereo.Down, m.GetBond(m.Atoms[1], m.Atoms[6]).Stereo);
}
public void ClockwiseSortShouldHandleExactlyOppositeAtoms()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 0, 4.50d, -14.84d));
m.Atoms.Add(Atom("C", 3, 4.51d, -13.30d));
m.Atoms.Add(Atom("C", 2, 4.93d, -14.13d));
m.Atoms.Add(Atom("C", 2, 3.68d, -14.81d));
m.Atoms.Add(Atom("O", 0, 4.05d, -15.54d));
m.Atoms.Add(Atom("O", 1, 3.23d, -15.50d));
m.Atoms.Add(Atom("C", 3, 5.32d, -14.86d));
m.Atoms.Add(Atom("C", 3, 4.45d, -16.27d));
m.AddBond(m.Atoms[0], m.Atoms[2], BondOrder.Single);
m.AddBond(m.Atoms[2], m.Atoms[1], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[3], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[6], BondOrder.Single);
m.AddBond(m.Atoms[7], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[3], BondOrder.Single);
m.StereoElements.Add(new TetrahedralChirality(m.Atoms[0], new IAtom[] { m.Atoms[2], m.Atoms[4], m.Atoms[6], m.Atoms[3], }, TetrahedralStereo.AntiClockwise));
NonplanarBonds.Assign(m);
Assert.AreEqual(BondStereo.Up, m.Bonds[2].Stereo);
}
public void UseCrossedBondIfNeeded()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 3, 0.000, 0.000));
m.Atoms.Add(Atom("C", 1, 1.299, -0.750));
m.Atoms.Add(Atom("C", 1, 2.598, -0.000));
m.Atoms.Add(Atom("C", 1, 3.897, -0.750));
m.Atoms.Add(Atom("C", 1, 5.196, -0.000));
m.Atoms.Add(Atom("C", 1, 6.495, -0.750));
m.Atoms.Add(Atom("C", 1, 7.794, -0.000));
m.Atoms.Add(Atom("C", 3, 9.093, -0.750));
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.Single);
m.AddBond(m.Atoms[3], m.Atoms[4], BondOrder.Double);
m.AddBond(m.Atoms[4], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[5], m.Atoms[6], BondOrder.Double);
m.AddBond(m.Atoms[6], m.Atoms[7], BondOrder.Single);
m.StereoElements.Add(new DoubleBondStereochemistry(
m.Bonds[1],
new IBond[] {
m.Bonds[0],
m.Bonds[2]
},
DoubleBondConformation.Opposite));
m.StereoElements.Add(new DoubleBondStereochemistry(
m.Bonds[5],
new IBond[] {
m.Bonds[4],
m.Bonds[6]
},
DoubleBondConformation.Opposite));
NonplanarBonds.Assign(m);
Assert.AreEqual(BondStereo.EOrZ, m.Bonds[3].Stereo);
}
public void Anticlockwise_1()
{
var m = new AtomContainer();
m.Atoms.Add(Atom("C", 0, -1.47d, 3.62d));
m.Atoms.Add(Atom("C", 2, -1.13d, 2.16d));
m.Atoms.Add(Atom("C", 2, 0.30d, 1.72d));
m.Atoms.Add(Atom("C", 3, 0.64d, 0.26d));
m.Atoms.Add(Atom("C", 3, -2.90d, 4.06d));
m.Atoms.Add(Atom("N", 2, 0.03d, 3.70d));
m.Atoms.Add(Atom("O", 1, -1.28d, 5.11d));
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[0], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[5], BondOrder.Single);
m.AddBond(m.Atoms[0], m.Atoms[6], BondOrder.Single);
m.StereoElements.Add(new TetrahedralChirality(m.Atoms[0], new IAtom[] { m.Atoms[1], m.Atoms[4], m.Atoms[5], m.Atoms[6] }, TetrahedralStereo.AntiClockwise));
NonplanarBonds.Assign(m);
Assert.AreEqual(BondStereo.None, m.Bonds[0].Stereo);
Assert.AreEqual(BondStereo.None, m.Bonds[3].Stereo);
Assert.AreEqual(BondStereo.Down, m.Bonds[4].Stereo);
Assert.AreEqual(BondStereo.Up, m.Bonds[5].Stereo);
}
