/// <summary>
/// <para>Sorts the IAtomContainers in the given IAtomContainerSet by the following
/// criteria with decreasing priority:</para>
/// <list type="bullet">
/// <item>Compare atom count</item>
/// <item>Compare molecular weight (heavy atoms only)</item>
/// <item>Compare bond count</item>
/// <item>Compare sum of bond orders (heavy atoms only)</item>
/// </list>
/// <para>If no difference can be found with the above criteria, the IAtomContainers are
/// considered equal.</para>
/// </summary>
/// <param name="atomContainerSet">The collection of IAtomContainer objects</param>
public static void Sort <T>(IChemObjectSet <T> atomContainerSet) where T : IAtomContainer
{
var atomContainerList = atomContainerSet.ToList();
atomContainerList.Sort(new AtomContainerComparator <T>());
atomContainerSet.Clear();
foreach (var anAtomContainerList in atomContainerList)
{
atomContainerSet.Add(anAtomContainerList);
}
}
internal IAtomContainer Generate2(IChemObjectSet <IAtomContainer> atomContainers)
{
int iteration = 0;
bool structureFound = false;
do
{
iteration++;
bool bondFormed;
do
{
bondFormed = false;
var atomContainersArray = atomContainers.ToList();
for (var atomContainersArrayIndex = 0; atomContainersArrayIndex < atomContainersArray.Count; atomContainersArrayIndex++)
{
var ac = atomContainersArray[atomContainersArrayIndex];
if (ac == null)
{
continue;
}
var atoms = ac.Atoms.ToList(); // ToList is required because some atoms are added to ac.Atoms in the loop.
foreach (var atom in atoms)
{
if (!satCheck.IsSaturated(atom, ac))
{
var partner = GetAnotherUnsaturatedNode(atom, ac, atomContainers);
if (partner != null)
{
var toadd = AtomContainerSetManipulator.GetRelevantAtomContainer(atomContainers, partner);
var cmax1 = satCheck.GetCurrentMaxBondOrder(atom, ac);
var cmax2 = satCheck.GetCurrentMaxBondOrder(partner, toadd);
var max = Math.Min(cmax1, cmax2);
var order = Math.Min(Math.Max(1, max), 3); //(double)Math.Round(Math.Random() * max)
Debug.WriteLine($"cmax1, cmax2, max, order: {cmax1}, {cmax2}, {max}, {order}");
if (toadd != ac)
{
var indexToRemove = atomContainersArray.IndexOf(toadd);
if (indexToRemove != -1)
{
atomContainersArray[indexToRemove] = null;
}
atomContainers.Remove(toadd);
ac.Add(toadd);
}
ac.Bonds.Add(ac.Builder.NewBond(atom, partner, BondManipulator.CreateBondOrder(order)));
bondFormed = true;
}
}
}
}
} while (bondFormed);
if (atomContainers.Count == 1 &&
satCheck.IsSaturated(atomContainers[0]))
{
structureFound = true;
}
} while (!structureFound && iteration < 5);
if (atomContainers.Count == 1 && satCheck.IsSaturated(atomContainers[0]))
{
structureFound = true;
}
if (!structureFound)
{
return(null);
}
return(atomContainers[0]);
}
