private AtomContainer GetBunchOfUnbondedAtoms()
{
IAtomContainer molecule = TestMoleculeFactory.MakeAlphaPinene();
FixCarbonHCount(molecule);
molecule.RemoveAllElectronContainers();
return((AtomContainer)molecule);
}
/// <summary>
/// Generates a random structure based on the atoms in the given <see cref="IAtomContainer"/>.
/// </summary>
public IAtomContainer Generate()
{
int iteration = 0;
bool structureFound = false;
do
{
iteration++;
atomContainer.RemoveAllElectronContainers();
bool bondFormed;
do
{
bondFormed = false;
foreach (var atom in atomContainer.Atoms)
{
if (!satCheck.IsSaturated(atom, atomContainer))
{
var partner = GetAnotherUnsaturatedNode(atom);
if (partner != null)
{
var cmax1 = satCheck.GetCurrentMaxBondOrder(atom, atomContainer);
var cmax2 = satCheck.GetCurrentMaxBondOrder(partner, atomContainer);
var max = Math.Min(cmax1, cmax2);
var order = Math.Min(Math.Max(1.0, random.NextInt((int)Math.Round(max))), 3.0);
Debug.WriteLine($"Forming bond of order {order}");
atomContainer.Bonds.Add(atomContainer.Builder.NewBond(atom, partner, BondManipulator.CreateBondOrder(order)));
bondFormed = true;
}
}
}
} while (bondFormed);
if (ConnectivityChecker.IsConnected(atomContainer) && satCheck.IsSaturated(atomContainer))
{
structureFound = true;
}
} while (!structureFound && iteration < 20);
Debug.WriteLine($"Structure found after #iterations: {iteration}");
return(atomContainer.Builder.NewAtomContainer(atomContainer));
}