public void TestNewSaturate_methylamine_radical_cation()
{
// test Ammonia, CH3NH3+
Atom c = new Atom("C")
{
ImplicitHydrogenCount = 3
};
Atom n = new Atom("N")
{
ImplicitHydrogenCount = 3,
FormalCharge = +1
};
Bond b1 = new Bond(c, n, BondOrder.Single);
var m = new AtomContainer();
m.Atoms.Add(c);
m.Atoms.Add(n);
m.Bonds.Add(b1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
CDK.LonePairElectronChecker.Saturate(m);
Assert.AreEqual(0, m.GetConnectedLonePairs(n).Count());
}
public void TestNewSaturate_Methyl_alcohol_protonated()
{
// test Methyl alcohol protonated, CH3OH2+
Atom c1 = new Atom("C")
{
ImplicitHydrogenCount = 3
};
Atom o = new Atom("O")
{
FormalCharge = +1,
ImplicitHydrogenCount = 2
};
Bond b1 = new Bond(c1, o, BondOrder.Single);
var m = new AtomContainer();
m.Atoms.Add(c1);
m.Atoms.Add(o);
m.Bonds.Add(b1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
CDK.LonePairElectronChecker.Saturate(m);
Assert.AreEqual(1, m.GetConnectedLonePairs(o).Count());
}
public void TestNewSaturate_Methyl_chloride()
{
// test Methyl chloride, CH3Cl
Atom c1 = new Atom("C")
{
ImplicitHydrogenCount = 3
};
Atom cl = new Atom("Cl");
Bond b1 = new Bond(c1, cl, BondOrder.Single);
var m = new AtomContainer();
m.Atoms.Add(c1);
m.Atoms.Add(cl);
m.Bonds.Add(b1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
CDK.LonePairElectronChecker.Saturate(m);
Assert.AreEqual(3, m.GetConnectedLonePairs(cl).Count());
Assert.AreEqual(0, m.GetConnectedLonePairs(c1).Count());
}
public void TestNewSaturate_Methyl_alcohol_AddH()
{
// test Methyl alcohol, CH3OH
var m = new AtomContainer();
m.Atoms.Add(new Atom("C"));
m.Atoms.Add(new Atom("O"));
for (int i = 0; i < 4; i++)
{
m.Atoms.Add(new Atom("H"));
}
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.AddBond(m.Atoms[0], m.Atoms[4], BondOrder.Single);
m.AddBond(m.Atoms[1], m.Atoms[5], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
CDK.LonePairElectronChecker.Saturate(m);
Assert.AreEqual(2, m.GetConnectedLonePairs(m.Atoms[1]).Count());
Assert.AreEqual(0, m.GetConnectedLonePairs(m.Atoms[0]).Count());
}
public void TestNewSaturate_Ammonia()
{
// test Ammonia, H3N
Atom n = new Atom("N")
{
ImplicitHydrogenCount = 3
};
var m = new AtomContainer();
m.Atoms.Add(n);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
CDK.LonePairElectronChecker.Saturate(m);
Assert.AreEqual(1, m.GetConnectedLonePairs(n).Count());
}
public void TestNewSaturate_methoxide_anion()
{
// test methoxide anion, CH3O-
Atom c1 = new Atom("C")
{
ImplicitHydrogenCount = 3
};
Atom o = new Atom("O")
{
FormalCharge = -1
};
Bond b1 = new Bond(c1, o, BondOrder.Single);
var m = new AtomContainer();
m.Atoms.Add(c1);
m.Atoms.Add(o);
m.Bonds.Add(b1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
CDK.LonePairElectronChecker.Saturate(m);
Assert.AreEqual(3, m.GetConnectedLonePairs(o).Count());
}