public void TestAromaticSaturation()
{
var mol = builder.NewAtomContainer();
mol.Atoms.Add(builder.NewAtom("C")); // 0
mol.Atoms.Add(builder.NewAtom("C")); // 1
mol.Atoms.Add(builder.NewAtom("C")); // 2
mol.Atoms.Add(builder.NewAtom("C")); // 3
mol.Atoms.Add(builder.NewAtom("C")); // 4
mol.Atoms.Add(builder.NewAtom("C")); // 5
mol.Atoms.Add(builder.NewAtom("C")); // 6
mol.Atoms.Add(builder.NewAtom("C")); // 7
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single); // 1
mol.AddBond(mol.Atoms[1], mol.Atoms[2], BondOrder.Single); // 2
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Single); // 3
mol.AddBond(mol.Atoms[3], mol.Atoms[4], BondOrder.Single); // 4
mol.AddBond(mol.Atoms[4], mol.Atoms[5], BondOrder.Single); // 5
mol.AddBond(mol.Atoms[5], mol.Atoms[0], BondOrder.Single); // 6
mol.AddBond(mol.Atoms[0], mol.Atoms[6], BondOrder.Single); // 7
mol.AddBond(mol.Atoms[6], mol.Atoms[7], BondOrder.Triple); // 8
for (int f = 0; f < 6; f++)
{
mol.Atoms[f].IsAromatic = true;
mol.Atoms[f].Hybridization = Hybridization.SP2;
mol.Bonds[f].IsAromatic = true;
}
FindAndConfigureAtomTypesForAllAtoms(mol);
adder.AddImplicitHydrogens(mol);
Assert.AreEqual(6, AtomContainerManipulator.GetTotalHydrogenCount(mol));
}
/// <summary>
/// </summary>
/// <param name="set">The collection of IAtomContainer objects</param>
/// <returns>The summed implicit hydrogens of all atoms in this set.</returns>
public static int GetTotalHydrogenCount(IEnumerable <IAtomContainer> set)
{
int hCount = 0;
foreach (var item in set)
{
hCount += AtomContainerManipulator.GetTotalHydrogenCount(item);
}
return(hCount);
}
public void TestNaCl()
{
var mol = builder.NewAtomContainer();
var cl = builder.NewAtom("Cl");
cl.FormalCharge = -1;
mol.Atoms.Add(cl);
var na = builder.NewAtom("Na");
na.FormalCharge = +1;
mol.Atoms.Add(na);
FindAndConfigureAtomTypesForAllAtoms(mol);
adder.AddImplicitHydrogens(mol);
Assert.AreEqual(2, mol.Atoms.Count);
Assert.AreEqual(0, AtomContainerManipulator.GetTotalHydrogenCount(mol));
Assert.AreEqual(0, mol.GetConnectedBonds(cl).Count());
Assert.AreEqual(0, cl.ImplicitHydrogenCount.Value);
Assert.AreEqual(0, mol.GetConnectedBonds(na).Count());
Assert.AreEqual(0, na.ImplicitHydrogenCount.Value);
}
public void TestAdenine()
{
var mol = builder.NewAtomContainer(); // Adenine
IAtom a1 = mol.Builder.NewAtom("C");
a1.Point2D = new Vector2(21.0223, -17.2946);
mol.Atoms.Add(a1);
IAtom a2 = mol.Builder.NewAtom("C");
a2.Point2D = new Vector2(21.0223, -18.8093);
mol.Atoms.Add(a2);
IAtom a3 = mol.Builder.NewAtom("C");
a3.Point2D = new Vector2(22.1861, -16.6103);
mol.Atoms.Add(a3);
IAtom a4 = mol.Builder.NewAtom("N");
a4.Point2D = new Vector2(19.8294, -16.8677);
mol.Atoms.Add(a4);
IAtom a5 = mol.Builder.NewAtom("N");
a5.Point2D = new Vector2(22.2212, -19.5285);
mol.Atoms.Add(a5);
IAtom a6 = mol.Builder.NewAtom("N");
a6.Point2D = new Vector2(19.8177, -19.2187);
mol.Atoms.Add(a6);
IAtom a7 = mol.Builder.NewAtom("N");
a7.Point2D = new Vector2(23.4669, -17.3531);
mol.Atoms.Add(a7);
IAtom a8 = mol.Builder.NewAtom("N");
a8.Point2D = new Vector2(22.1861, -15.2769);
mol.Atoms.Add(a8);
IAtom a9 = mol.Builder.NewAtom("C");
a9.Point2D = new Vector2(18.9871, -18.0139);
mol.Atoms.Add(a9);
IAtom a10 = mol.Builder.NewAtom("C");
a10.Point2D = new Vector2(23.4609, -18.8267);
mol.Atoms.Add(a10);
IBond b1 = mol.Builder.NewBond(a1, a2, BondOrder.Double);
mol.Bonds.Add(b1);
IBond b2 = mol.Builder.NewBond(a1, a3, BondOrder.Single);
mol.Bonds.Add(b2);
IBond b3 = mol.Builder.NewBond(a1, a4, BondOrder.Single);
mol.Bonds.Add(b3);
IBond b4 = mol.Builder.NewBond(a2, a5, BondOrder.Single);
mol.Bonds.Add(b4);
IBond b5 = mol.Builder.NewBond(a2, a6, BondOrder.Single);
mol.Bonds.Add(b5);
IBond b6 = mol.Builder.NewBond(a3, a7, BondOrder.Double);
mol.Bonds.Add(b6);
IBond b7 = mol.Builder.NewBond(a3, a8, BondOrder.Single);
mol.Bonds.Add(b7);
IBond b8 = mol.Builder.NewBond(a4, a9, BondOrder.Double);
mol.Bonds.Add(b8);
IBond b9 = mol.Builder.NewBond(a5, a10, BondOrder.Double);
mol.Bonds.Add(b9);
IBond b10 = mol.Builder.NewBond(a6, a9, BondOrder.Single);
mol.Bonds.Add(b10);
IBond b11 = mol.Builder.NewBond(a7, a10, BondOrder.Single);
mol.Bonds.Add(b11);
FindAndConfigureAtomTypesForAllAtoms(mol);
adder.AddImplicitHydrogens(mol);
Assert.AreEqual(5, AtomContainerManipulator.GetTotalHydrogenCount(mol));
}
